Methods for detecting peptide/mhc/tcr binding

ABSTRACT

Provided herein are compositions and methods for detecting the binding of a peptide to an MHC molecule, and the binding of a peptide:MHC complex to a TCR. In preferred embodiments, the compositions and methods are in a highly-multiplexed way. The compositions and methods disclosed herein can be used to provide direct information on which peptides are bound to an MHC molecule. Also provided is a method for simultaneously detecting a large number of peptides for binding to an MHC molecule and/or a T cell. A method for detecting competitive binding of a large number of peptides to an MHC molecule and/or a T cell is also disclosed. Also provided herein is a method for simultaneously detecting a large number of specific TCRs. The compositions and methods of the present invention are useful for vaccine design, research and monitoring of autoimmune and infectious disease, immunogenicity testing of therapeutics, and tissue typing.

RELATED APPLICATION

This application is a continuation of U.S. Ser. No. 14/776,537, which isa U.S. National Stage Application of International Application No. PCT/US2014/029691, filed Mar. 14, 2014, which claims priority to U.S.Provisional Patent Application Ser. No. 61/800,891, filed on Mar. 15,2013. The contents of the above-identified applications are incorporatedby reference herein in their entireties for all purposes.

SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE

The content of the following submission on ASCII text file isincorporated herein by reference in its entirety: a computer readableform (CRF) of the Sequence Listing (file name: 699932000101SeqList.txt,date recorded: May 21, 2019, size: 1.93 KB).

TECHNICAL FIELD

The present invention is in the field of immunology, and relates toprotein interactions in the immune system. Specifically, the presentinvention relates to peptide-MHC interactions and methods andcompositions for detecting the interactions.

BACKGROUND

Immunology is fundamentally concerned with the interaction between ahost, an organism whose immune system mounts a response; and animmunogen, the agent against which that response is directed. Theoutcome of this interaction dictates the host's fate: for a pathogenicimmunogen, infection; for an altered-self immunogen, cancer; for a selfimmunogen, autoimmunity; and for an innocuous environmental immunogen,allergy. Improvements in DNA sequencing capacity have provided tools toexplore the genetic basis of these different immune outcomes athigh-resolution and with broad-coverage, with reference to both host andimmunogen genomes (Peng et al., 2009, Curr. Opin. Microbiol. 12:432-438; Benichou et al., 2012, Immunology 135: 183-191).

One of the most important protein interface between the host andimmunogen is the peptide:major histocompatibility (p:MHC) complex, whichcomprises a host-encoded transmembrane protein (MHC) in physicalassociation with an immunogen-derived peptide. This complex serves twoparallel systems of antigen presentation: (1) the cytosolic pathway, inwhich endogenous proteins are processed into short peptides, e.g.,peptides of approximately 7-10 amino acids, and presented in complexwith MHC class I by all nucleated cells; and (2) the endosomal pathway,in which engulfed exogenous proteins are processed into peptides ofapproximately 10-25 amino acids and presented in complex with MHC classII by specialized antigen presenting cells (Germain, 1994, Cell 76:287-299). Once presented to the adaptive immune system in one of theseways, immunogen-derived peptides can trigger a highly antigen-specificresponse, for example, a cellular immune response versus a humoralimmune response, or an immunogenic response versus a tolerogenicresponse.

SUMMARY OF THE INVENTION

Compositions and methods for detecting peptide/MHC binding aredisclosed. Provided herein is an MHC-binding peptide conjugated to apolynucleotide. In certain embodiments, the polynucleotide can be DNA,cDNA, RNA, mRNA, rRNA, tRNA, PNA, a DNA-like molecule or an RNA-likemolecule.

Also provided is a library of at least two MHC-binding peptides eachconjugated to a polynucleotide, wherein each said polynucleotide isidentified by a probe that specifically binds to said polynucleotide. Incertain embodiments, the polynucleotide and the probe can be DNA, cDNA,RNA, mRNA, rRNA, tRNA, PNA, a DNA-like molecule or an RNA-like molecule.

Provided herein is a composition comprising at least two MHC-bindingpeptides each conjugated to a polynucleotide, wherein the at least twoMHC-binding peptides are multimerized or oligomerized. In one aspect,the at least two MHC-binding peptides are conjugated to the samepolynucleotide and are thus multimerized or oligomerized. In otherembodiments, the at least two MHC-binding peptides are each conjugatedto a separate polynucleotide, wherein the polynucleotides mediate themultimerization or oligomerization of the at least two MHC-bindingpeptides. In some embodiments, the multimerization or oligomerization ismediation by nucleotide sequence complementarity.

In one embodiment, a method for detecting binding of a peptide to an MHCmolecule is disclosed. The method comprises: contacting said MHCmolecule with a polynucleotide-peptide conjugate, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide; contacting said polynucleotide-peptide conjugate with aprobe that specifically binds to said polynucleotide; detecting bindingof said probe to said polynucleotide; and, correlating binding of saidprobe to said polynucleotide with binding of said peptide to said MHCmolecule.

In another embodiment, a method for simultaneously detecting binding ofa library of peptides to an MHC molecule is provided. The methodcomprises: providing a polynucleotide-peptide conjugate for each saidpeptide, said polynucleotide-peptide conjugate comprising said peptideand a polynucleotide; contacting said MHC molecule with a pool of saidpolynucleotide-peptide conjugates; contacting each of saidpolynucleotide-peptide conjugate with a probe that specifically binds toeach said polynucleotide; detecting binding of said probe to eachcorresponding polynucleotide that each said probe specifically binds;and correlating binding of said probe to each correspondingpolynucleotide with binding of each corresponding peptide to said MHCmolecule. In another embodiment, the method further comprises comparingbinding, for example, in terms of binding specificity and/or bindingaffinity, of each said peptide to said MHC molecule, among the peptidesin said library.

In yet another embodiment, provided herein is a method for detecting ina library of peptides competitive binding of each said peptide to an MHCmolecule, comprising: providing a polynucleotide-peptide conjugate foreach said peptide, said polynucleotide-peptide conjugate comprising saidpeptide and a polynucleotide; contacting said MHC molecule with a poolof said polynucleotide-peptide conjugates; contacting each of saidpolynucleotide-peptide conjugate with a probe that specifically binds toeach said polynucleotide; detecting binding of said probe to eachcorresponding polynucleotide that each said probe specifically binds;and correlating binding of said probe to each correspondingpolynucleotide with binding of each corresponding peptide to said MHCmolecule, wherein said peptides compete for binding of said MHCmolecule. In another embodiment, the method further comprises comparingbinding, for example, in terms of binding specificity and/or bindingaffinity, of each said peptide to said MHC molecule, among the peptidesin said library.

In one aspect, disclosed herein is a method for detecting binding of apeptide to a T cell, comprising: contacting said T cell with an MHCmolecule and a polynucleotide-peptide conjugate, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide; contacting said polynucleotide-peptide conjugate with aprobe that specifically binds to said polynucleotide; detecting bindingof said probe to said polynucleotide; and, correlating binding of saidprobe to said polynucleotide with binding of said peptide to said Tcell.

In another aspect, a method for simultaneously detecting binding of alibrary of peptides to a T cell is provided. This method comprises:providing a polynucleotide-peptide conjugate for each said peptide, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide; contacting said T cell with a pool of saidpolynucleotide-peptide conjugates and an MHC molecule; contacting eachof said polynucleotide-peptide conjugate with a probe that specificallybinds to each said polynucleotide; detecting binding of said probe toeach corresponding polynucleotide that each said probe specificallybinds; and correlating binding of said probe to each correspondingpolynucleotide with binding of each corresponding peptide to said Tcell. In one embodiment, the peptide of the present invention binds aTCR of said T cell.

In yet another aspect, described herein is a method for detecting in alibrary of peptides competitive binding of each said peptide to a Tcell, comprising: providing a polynucleotide-peptide conjugate for eachsaid peptide, said polynucleotide-peptide conjugate comprising saidpeptide and a polynucleotide; contacting said T cell with a pool of saidpolynucleotide-peptide conjugates and an MHC molecule; contacting eachof said polynucleotide-peptide conjugate with a probe that specificallybinds to each said polynucleotide; detecting binding of said probe toeach corresponding polynucleotide that each said probe specificallybinds; and correlating binding of said probe to each correspondingpolynucleotide with binding of each corresponding peptide to said Tcell, wherein said peptides compete for binding of said MHC molecule andsaid T cell. In one embodiment, the peptide binds a TCR of said T cell.

In any of the embodiments or any combination thereof, the TCR can be aTCR on a T cell, a soluble TCR, an isolated TCR, and an immobilized TCR.Any functional fragment or portion of a TCR is also encompassed by thepresent invention.

In any of the embodiments or any combination thereof, the method of thepresent invention can further comprise comparing the detected binding ofsaid peptide to said MHC molecule, said T cell, or said TCR with areference. In a further embodiment, the method of the present inventionas disclosed in any of the embodiments or any combination thereoffurther comprises selecting the detected binding of said peptide over areference, for the purposes of identifying antigens in infection,autoimmunity, allergy, or cancer, or for vaccine design.

In any of the embodiments or any combination thereof, the polynucleotideand the probe are selected from the group consisting of DNA, cDNA, RNA,mRNA, rRNA, tRNA, PNA, a DNA-like molecule or an RNA-like molecule. Inany of the embodiments or any combination thereof, the binding of saidprobe to said polynucleotide can be detected by gel electrophoresis,hybridization, PCR, qPCR, or nucleotide sequencing.

In the method of the present invention as disclosed in any of theembodiments or any combination thereof, the MHC molecule can beimmobilized. In another embodiment, said polynucleotide-peptideconjugate is multimerized or oligomerized in the method of the presentinvention as disclosed in any of the embodiments or any combinationthereof. In yet another embodiment, the method of the present inventionis performed in a high throughput fashion.

In any of the embodiments disclosed herein, a method of the presentdisclosure further comprises one or more of the steps of: allowingbinding between the polynucleotide-peptide conjugate and the MHCmolecule to reach equilibrium; washing the complex formed between thepolynucleotide-peptide conjugate and the MHC molecule under a suitablecondition to remove unbound or non-specifically boundpolynucleotide-peptide conjugate; allowing the complex between thepolynucleotide-peptide conjugate and the MHC molecule to dissociate, forexample, for a suitable period of time; and detecting thepolynucleotide-peptide conjugate that remains bound to the MHC molecule.

In any of the preceding embodiments, the complex between thepolynucleotide-peptide conjugate and the MHC molecule can be allowed todissociate in the presence of one or more blocker species. In oneaspect, the one or more blocker species prevent binding or reassociationof the polynucleotide-peptide conjugate to the MHC molecule. In someembodiments, the blocker species compete with the polynucleotide-peptideconjugate for binding to the MHC molecule. In one aspect, the bindingbetween the blocker species and the MHC complex does not generate asignal indicative of specific binding between the polynucleotide-peptideconjugate and the MHC molecule.

In any of the embodiments disclosed herein, the binding of thepolynucleotide-peptide conjugate to the MHC molecule can occur in thepresence of one or more chaperons. In some embodiments, the chaperon isselected from the group consisting of a protein chaperon, a chemicalchaperon, HLA-DM and an analogue thereof, a small molecule that has thesame or similar chaperon function as HLA-DM, parachlorophenol (pCP) andan analogue thereof, and dimethylsulphoxide (DMSO) and an analoguethereof.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 (upper panel) shows a multiplexed peptide-MHC binding assay. MHCmolecules are tested in a pooled binding reaction against a set of insilico-programmed peptide-cDNA conjugates. Bound peptides are identifiedby high throughput DNA sequencing, which has the dynamic range to revealthe spectrum of differentially-competitive MHC binders (illustrated herein the order triangle>circle>square).

FIG. 1 (lower panel) shows a multiplexed assay for T cell specificitydetection. MHC molecules are incubated with multivalent peptide-cDNAconjugates and a biological sample containing T cells. T cell boundpeptide cDNA:MHC complexes are then isolated and detected by highthroughput sequencing.

FIG. 2 shows the use of the multiplexed peptide-MHC binding assay withpooled “eigenpeptides” to report individuals' HLA information. HLAmolecules are isolated from the blood of donors with different HLAgenotypes and tested against a complex pool of peptide-cDNA conjugates.This pool is designed with the aid of the IEDB to cover all listed humanhaplotypes, with an emphasis on peptides that bind HLA molecules asuniquely as possible (“eigenpeptides”). Next generation sequencing ofbound peptide-cDNA conjugates provides information about the HLAmolecules that are present. In this example, the two depictedindividuals share 1 out of their 2 HLA haplotypes.

FIG. 3A shows a representative method for peptide-cDNA pool production.Oligonucleotide sequences of choice are designed in silico, cheaplyproduced by parallel synthesis on an array, released, and then convertedinto peptide-cDNA conjugates.

FIG. 3B shows a protease assay. Peptide-cDNA conjugate pools areimmobilized on beads, treated with a protease, and the cleaved speciesare detected by sequencing of the released cDNAs.

FIGS. 4A-4B show sequence-specific binding of peptide-cDNA conjugates toMHC molecules. Peptide-cDNA conjugates with the sequences YKTIAFDEEARR(“YK”) (SEQ ID NO: 1) or YPKYVKQNTLKLAT (“YP”) (SEQ ID NO: 2) wereincubated either alone (“none”), or in the presence of biotinylatedHLA-DR1 (“DR1”) or HLA-DR3 (“DR3”) MHC molecules. Following incubation,binding complexes were captured on streptavidin beads, washed, andeluted. Eluted DNA was imaged by gel electrophoresis (FIG. 4A), andquantified by qPCR (FIG. 4B). The peptides YKTIAFDEEARR (SEQ ID NO: 1)and YPKYVKQNTLKLAT (SEQ ID NO: 2) are known to bind the DR3 and DR1molecules, respectively.

FIG. 5 shows multiplex binding of peptide-cDNA conjugates to an MHCmolecules. Peptide-cDNA conjugates with the sequences YPKYVKQNTLKLAT(“YP (WT)”) (SEQ ID NO: 3), YPKYVKQNTLKLAA (“YP (T14A)”) (SEQ ID NO: 4),and YPKAVKQNTLKLAT (“YP (Y4A)”) (SEQ ID NO: 5) were produced by in vitrotranscription and translation from DNA templates. The three peptide-cDNAconjugates were then incubated, either individually (“1-plex”) or mixedin equal ratios (“3-plex”), together with biotinylated HLA-DR1 (“DR1”)MHC molecules. Following incubation, binding complexes were captured onstreptavidin beads, washed, and eluted. Eluted DNA was quantified byqPCR. The peptides YPKYVKQNTLKLAT (SEQ ID NO: 3), YPKYVKQNTLKLAA (SEQ IDNO: 4) and YPKAVKQNTLKLAT (SEQ ID NO: 5) are known to bind the DR1molecule with high, high and low affinities, respectively.

FIGS. 6A-6C show assay conditions for detection of specific peptide:MHCbinding according to certain embodiments of the present disclosure.

FIGS. 7A-7C show detection of specific peptide:MHC binding in a pool ofpolynucleotide-peptide conjugates, according to certain embodiments ofthe present disclosure.

FIGS. 8A-8B show detection of specific peptide:MHC binding using theextension assay format, according to certain embodiments of the presentdisclosure.

DETAILED DESCRIPTION A. Definitions

Unless defined otherwise, all terms of art, notations and othertechnical and scientific terms or terminology used herein are intendedto have the same meaning as is commonly understood by one of ordinaryskill in the art to which this invention pertains. In some cases, termswith commonly understood meanings are defined herein for clarity and/orfor ready reference, and the inclusion of such definitions herein shouldnot necessarily be construed to represent a substantial difference overwhat is generally understood in the art. Many of the techniques andprocedures described or referenced herein are well understood andcommonly employed using conventional methodology by those skilled in theart.

All publications, including patent documents, scientific articles anddatabases, referred to in this application and the bibliography andattachments are incorporated by reference in their entirety for allpurposes to the same extent as if each individual publication wereindividually incorporated by reference. If a definition set forth hereinis contrary to or otherwise inconsistent with a definition set forth inthe patents, applications, published applications and other publicationsthat are herein incorporated by reference, the definition set forthherein prevails over the definition that is incorporated herein byreference.

Although methods and materials similar or equivalent to those describedherein can be used in the practice or testing of the present disclosure,suitable methods and materials are described below. The materials,methods, and examples are illustrative only and not intended to belimiting. Other features of the disclosure are apparent from thefollowing detailed description and the claims. In the followingdescription of certain embodiments provided here, reference is made tothe accompanying drawings which form a part hereof, and in which it isshown by way of illustration specific embodiments in which the inventioncan be practiced. It is to be understood that other embodiments can beused and structural changes can be made without departing from the scopeof the invention.

The practice of the provided embodiments will employ, unless otherwiseindicated, conventional techniques of molecular biology and the like,which are within the skill of the art. Such techniques are explainedfully in the literature. See e.g., Molecular Cloning: A LaboratoryManual, (J. Sambrook et al., Cold Spring Harbor Laboratory, Cold SpringHarbor, N.Y., 1989); Current Protocols in Molecular Biology (F. Ausubelet al. eds., 1987 and updated); Essential Molecular Biology (T. Browned., IRL Press 1991); Gene Expression Technology (Goeddel ed., AcademicPress 1991); Methods for Cloning and Analysis of Eukaryotic Genes (A.Bothwell et al. eds., Bartlett Publ. 1990); Gene Transfer and Expression(M. Kriegler, Stockton Press 1990); Recombinant DNA Methodology (R. Wuet al. eds., Academic Press 1989); PCR: A Practical Approach (M.McPherson et al., IRL Press at Oxford University Press 1991); CellCulture for Biochemists (R. Adams ed., Elsevier Science Publishers1990); Mammalian Cell Biotechnology (M. Butler ed., 1991); Animal CellCulture (J. Pollard et al. eds., Humana Press 1990); Culture of AnimalCells, 2nd Ed. (R. Freshney et al. eds., Alan R. Liss 1987); FlowCytometry and Sorting (M. Melamed et al. eds., Wiley-Liss 1990); theseries Methods in Enzymology (Academic Press, Inc.); Techniques inImmunocytochemistry, (G. Bullock & P. Petrusz eds., Academic Press 1982,1983, 1985, 1989); Handbook of Experimental Immunology, (D. Weir & C.Blackwell, eds.); Cellular and Molecular Immunology (A. Abbas et al., W.B. Saunders Co. 1991, 1994); Current Protocols in Immunology (J. Coliganet al. eds. 1991); the series Annual Review of Immunology; the seriesAdvances in Immunology; Oligonucleotide Synthesis (M. Gait ed., 1984);and Animal Cell Culture (R. Freshney ed., IRL Press 1987).

Throughout this disclosure, various aspects of this invention arepresented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible sub-ranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed sub-ranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 3, 4, 5, and 6. This appliesregardless of the breadth of the range.

As used herein, “a” or “an” means “at least one” or “one or more.”

“Individual” means any living organism, including humans and othermammals.

By “subject” is meant an organism to which the provided compositions,methods, kits, and devices can be administered or applied. In oneembodiment, the subject is a mammal or a cell, a tissue, an organ or apart of the mammal. Mammals include, but are not limited to, humans, andnon-human animals, including farm animals, sport animals, rodents andpets.

As used herein, a “composition” refers to any mixture of two or moreproducts or compounds. It may be a solution, a suspension, liquid,powder, a paste, aqueous, non-aqueous or any combination thereof.

A “polynucleotide” refers to a polymeric form of nucleotides of anylength, either ribonucleotides or deoxyribonucleotides, or analogsthereof This term refers to the primary structure of the molecule, andthus includes double- and single-stranded DNA, as well as double- andsingle-stranded RNA. It also includes modified polynucleotides such asmethylated and/or capped polynucleotides.

The terms “nucleic acid” and “nucleic acid sequence” refer tooligonucleotides, nucleotides, polynucleotides, and fragments of any ofthese, including DNA or RNA (e.g., mRNA, rRNA, tRNA) of genomic orsynthetic origin which may be single-stranded or double-stranded and mayrepresent a sense or antisense strand, to peptide nucleic acid (PNA), orto any DNA-like or RNA-like material, natural or synthetic in origin.The term encompasses nucleic acids, i.e., oligonucleotides, containingknown analogues of natural nucleotides, naturally occurring nucleicacids, synthetic nucleic acids, and recombinant nucleic acids.

“Recombinant,” as applied to a polynucleotide, means that thepolynucleotide is the product of various combinations of cloning,restriction and/or ligation steps, and other procedures that result in aconstruct that is distinct from a polynucleotide found in nature.

As used herein, “substantially pure” means sufficiently homogeneous toappear free of readily detectable impurities as determined by standardmethods of analysis, such as thin layer chromatography (TLC), gelelectrophoresis and high performance liquid chromatography (HPLC), usedby those of skill in the art to assess such purity, or sufficiently puresuch that further purification would not detectably alter the physicaland chemical properties, such as enzymatic and biological activities, ofthe substance.

Methods for purification of the compounds to produce substantiallychemically pure compounds are known to those of skill in the art. Asubstantially chemically pure compound may, however, be a mixture ofstereoisomers or isomers. In such instances, further purification mightincrease the specific activity of the compound.

As used herein, “biological activity” refers to the in vivo activitiesof a compound or physiological responses that result upon in vivoadministration of a compound, composition or other mixture. Biologicalactivity, thus, encompasses therapeutic effects and pharmaceuticalactivity of such compounds, compositions and mixtures. Biologicalactivities may be observed in vitro systems designed to test or use suchactivities.

As used herein, “production by recombinant means” refers to productionmethods that use recombinant nucleic acid methods that rely onwell-known methods of molecular biology for expressing proteins encodedby cloned nucleic acids.

As used herein, “substantially identical” to a product meanssufficiently similar so that the property of interest is sufficientlyunchanged so that the substantially identical product can be used inplace of the product.

As used herein, “equivalent,” when referring to two sequences of nucleicacids means that the two sequences in question encode the same sequenceof amino acids or equivalent proteins. It also encompasses those thathybridize under conditions of moderate, preferably high stringency,whereby the encoded protein retains desired properties.

As used herein, when “equivalent” is used in referring to two proteinsor peptides, it means that the two proteins or peptides havesubstantially the same amino acid sequence with only conservative aminoacid substitutions that do not substantially alter one or moreactivities or functions of the protein or peptide. When “equivalent”refers to a property, the property does not need to be present to thesame extent (e.g., two peptides can exhibit different rates of the sametype of enzymatic activity), but the activities are preferablysubstantially the same. “Complementary,” when referring to two nucleicacid molecules, means that the two sequences of nucleotides are capableof hybridizing, preferably with less than 25%, more preferably with lessthan 15%, even more preferably with less than 5%, most preferably withno mismatches between opposed nucleotides. Preferably the two moleculeswill hybridize under conditions of high stringency.

As used herein: “stringency of hybridization” in determining percentagemismatch is as follows: 1) high stringency: 0.1× SSPE, 0.1% SDS, 65° C.;2) medium stringency: 0.2× SSPE, 0.1% SDS, 50° C. (also referred to asmoderate stringency); and 3) low stringency: 1.0× SSPE, 0.1% SDS, 50° C.It is understood that equivalent stringencies may be achieved usingalternative buffers, salts and temperatures.

The term “substantially” identical or homologous or similar varies withthe context as understood by those skilled in the relevant art andgenerally means at least 70%, preferably means at least 80%, morepreferably at least 90%, and most preferably at least 95% identity.

The terms “polypeptide,” “peptide,” and “protein” are usedinterchangeably to refer to polymers of amino acids of any length. Theseterms also include proteins that are post-translationally modifiedthrough reactions that include glycosylation, acetylation andphosphorylation.

As used herein, a “fragment thereof” “region thereof” and “portionthereof” refer to fragments, regions and portions that substantiallyretain at least one function of the full length polypeptide.

The terms “mimetic”, “peptide mimetic” and “peptidomimetic” are usedinterchangeably herein, and generally refer to a peptide, partialpeptide or non-peptide molecule that mimics the tertiary bindingstructure or activity of a selected native peptide or protein functionaldomain (e.g., binding motif, including, but not limited to, an MHCmolecule or a portion or region thereof that specifically binds to apeptide).

Peptide mimetics include recombinantly and chemically modified peptides,and non-peptide agents. Knowing the binding and structural features ofthe provided peptide:MHC complexes and proteins thereof, one of skill inthe art can design peptidomimetics having equivalent, or substantiallyequivalent, structure and/or function, such as, for example, the same,about the same, greater, or lower binding affinity, compared to a givenmolecule or complex. The mimetics include those entirely composed ofsynthetic, non-natural analogues of amino acids, and chimeric moleculescomposed of natural peptide amino acids and non-natural analogs of aminoacids. The mimetics further include polypeptide incorporatingconservative amino acid substitutions, as long as such substitutionsalso do not substantially alter the mimetic's structure and/or activity.

The polypeptides and peptides provided herein, and polypeptides andpeptides used in the provided complexes, compositions, combinations andmethods, can contain “mimetic” (“peptidomimetic”) forms.

As used herein, a variant of a polypeptide (protein) or polynucleotide(namely a parent polypeptide or polynucleotide) is a protein orpolynucleotide that contains one or more alterations in the amino acidor nucleic acid sequence, respectively, compared to the amino acidsequence of the parent polypeptide or the nucleic acid sequence of theparent polynucleotide. Alterations in sequences include substitutions,including conservative substitutions, deletions, additions andinsertions, compared to the sequence of the polypeptide orpolynucleotide of interest. A “conservative” amino acid substitution isa substitution of an amino acid having similar structural or chemicalproperty compared to the corresponding amino acid in the parentpolypeptide. Non-conservative amino acid substitutions are those wherethe charge, hydrophobicity and/or bulk of the amino acid issubstantially altered. Typically, a variant polypeptide has at least 75%sequence identity, and preferably at least 80%, 85%, 90%, 95%, or 95%sequence identity sequence identity, to the basic sequence. There may beat least 80%, for example at least 85%, 90% or 95%, amino acid identityover a stretch of 40 or more, for example 60, 80, 100 or more,contiguous amino acids (“hard homology”).

Variants of polypeptides may be generated by conventional techniques,including either random or site-directed mutagenesis of DNA encoding thepolypeptide. The resultant DNA fragments are then cloned into suitableexpression hosts such as E. coli or mammalian cells using conventionaltechnology and clones that retain the desired activity are detected. Theterm “variant” also includes naturally occurring allelic variants.

“Derivative” refers to a polypeptide or polynucleotide that has beenderived from a parent polynucleotide or polypeptide the basic sequenceby modification, for example by conjugation or complexing with otherchemical or protein moieties or by post-translational modificationtechniques as would be understood in the art. Such derivatives includeamino acid deletions and/or additions to polypeptides or variantsthereof wherein said derivatives retain activity of the basic protein.

Other derivatives include modification to side chains, incorporation ofunnatural amino acids and/or their derivatives during peptide,polypeptide or protein synthesis and the use of crosslinking agents.

B. MHC, MHC Binding Peptides, and Their Implications for Diseases i. MHC

As used herein, the term “Major Histocompatibility Complex” and theabbreviation “MHC” means the complex of genes, found in all vertebrates,which function in signaling between lymphocytes and antigen presentingcells in normal immune responses by binding peptides and presenting themfor possible recognition by T cell receptors (TCRs). In a naturalsetting within the cell, MHC molecules may bind peptides in anintracellular processing compartment and present these peptides on thesurface of antigen presenting cells to T cells.

MHC proteins are generally classified into two categories: class I andclass II MHC proteins. As used herein, the term “MHC class I” or “classI” refers to Major Histocompatibility Complex class I proteins, bindingpeptides, or genes, and the term “MHC class II” or “class II” refers toMajor Histocompatibility Complex class II proteins, binding peptides, orgenes. The human MHC region, also referred to as HLA, is found onchromosome six and includes the class I gene region and the class IIgene region. The MHC class I gene region includes the class I α genesHLA-A, HLA-B and HLA-C. The MHC class II region includes the DP, DQ andDR subregions for Class II α chain and β chain genes (i.e., DPα, DPβ,DQα, DQβ, DRα, and DRβ).

An MHC class I protein is an integral membrane protein comprising aglycoprotein heavy chain (α chain), which has three extracellulardomains (i.e., α1, α2 and α3), a transmembrane domain, and a cytoplasmicdomain. An MHC class I α chain (or class I heavy chain) can be anynaturally occurring polypeptide, or one encoded by an artificiallymutated α chain gene, essentially corresponding to at least the α1 anda2 domains of one of the gene products of an MHC class I α gene (e.g.HLA-A, HLA-B or HLA-C gene). The transmembrane and cytoplasmic domainsmay be omitted while an MHC class I α chain retains biological activity.An MHC class I α chain can be any variant with and without the usualglycosylation of the α2 domain, or any allelic variant of a class I αgene, as well as any equivalents, including those which may be producedsynthetically or recombinantly by, for example, site-directedmutagenesis of a naturally occurring variant. An MHC class I moleculecan be a covalently or non-covalently joined complex of an MHC class I αchain and a soluble subunit called the β₂-microglobulin chain (alsoknown as the class I light chain, or the class I β chain). A class I βchain can be any naturally occurring polypeptide, or one encoded by anartificially mutated β₂-microglobulin gene, essentially corresponding tothe gene product of a β₂-microglobulin gene. A class I β chain can beany allelic variants of β₂-microglobulin, as well as any equivalents,including those which may be produced synthetically of recombinantly by,for example, site-directed mutagenesis of a naturally occurring variant.

An MHC class II protein is a heterodimeric integral membrane proteincomprising one a chain and one β chain. The a chain has twoextracellular domains (i.e., α1 and α2), a transmembrane domain, and acytoplasmic domain. The β chain contains two extracellular domains(i.e., β1 and β2), a transmembrane domain, and a cytoplasmic domain. AnMHC class II α chain (or class II heavy chain) can be any naturallyoccurring polypeptide, or one encoded by an artificially mutated a gene,essentially corresponding to at least the α1 and α2 extracellulardomains of one of the gene products of an MHC class II α gene. Thetransmembrane and cytoplasmic domains may be omitted while an MHC classII α chain retains biological activity. An MHC class II α chain can beany variant with and without the usual glycosylation of the α1 and a2domains, or any allelic variant of a class II α gene, as well as anyequivalents, including those which may be produced synthetically orrecombinantly by, for example, site-directed mutagenesis of a naturallyoccurring variant. An MHC class II molecule can be a covalently ornon-covalently joined complex of an MHC class II α chain and an MHCclass II β chain (also known as the class II light chain, or the classII β chain). A class II β chain can be any naturally occurringpolypeptide, or one encoded by an artificially mutated class II β gene,essentially corresponding to at least the β1 and β2 extracellular domainof one of the gene products of an MHC class II β gene. The transmembraneand cytoplasmic domains may be omitted while an MHC class II β chainretains biological activity. An MHC class II β chain can be any variantwith and without the usual glycosylation of the β1 domain, or anyallelic variant of a class II β gene, as well as any equivalents,including those which may be produced synthetically or recombinantly by,for example, site-directed mutagenesis of a naturally occurring variant.

Many mammalian MHC molecules, including human MHC molecules are wellknown in the art. Without being bound by any theory, any MHC class I orclass II molecules can be used in the present invention.

The terms “MHC-peptide complex,” “MHC-peptide molecule,” “peptide-MHCcomplex,” and “peptide-MHC molecule” are used interchangeably. Anyportion of an MHC protein that forms a functional peptide binding grooveand that has a peptide bound to the peptide binding groove can be thepeptide-MHC complex of the present invention. The terms “binding site,”“binding groove” and “binding domain” of an MHC molecule are usedinterchangeably unless specified otherwise. It is well known in the artthat the domain organization of class I and class II molecules forms theantigen binding site, or peptide binding groove. A peptide bindinggroove refers to a portion of an MHC protein that forms a cavity inwhich a peptide can bind. According to the present invention, “aportion” of an MHC chain refers to any portion of an MHC chain that issufficient to form a peptide binding groove upon association with asufficient portion of another chain of an MHC protein. The conformationof a peptide binding groove is capable of being altered upon binding ofan antigenic peptide to enable proper alignment of amino acid residuesimportant for T cell receptor (TCR) binding to the MHC protein and/orpeptide.

An MHC class I binding domain (or groove) is formed primarily by the α1and α2 domains of an MHC class I α chain. In a preferred embodiment, anMHC class I binding domain includes the α3 domain of an α chain andβ₂-microglobulin, which may function to stabilize the over-all structureof the MHC class I molecule. An MHC class I binding domain may also beessentially defined as the extracellular domain of an MHC class Imolecule. In certain aspects, a portion of the extracellular domain maybe omitted while retaining biological activity. For most MHC class Imolecules, interaction of the α and β chains can occur in the absence ofa peptide. However, the two chain complex of MHC class I is inherentlyunstable until the binding groove is filled with a peptide.

A peptide binding groove of a class II protein can comprise portions ofthe α1 and β1 domains. In one embodiment, an MHC class II binding domainminimally includes the α1 and β1 domains. In a preferred embodiment, anMHC class II binding domain includes the α2 and β2 domains, which arebelieved to stabilize the over-all structure of the MHC binding cleft.An MHC class II binding domain may also be essentially defined as theextracellular domain of an MHC class II molecule. In certain aspects, aportion of the extracellular domain may be omitted while retainingbiological activity.

In certain aspects, provided herein is a soluble MHC protein comprisingany portions of MHC chains suitable to form a peptide binding groove,including any suitable portion of the extracellular domains of an MHCchain. A soluble MHC protein lacks amino acid sequences capable ofanchoring the molecule into a lipid-containing substrate, such as an MHCtransmembrane domain and/or an MHC cytoplasmic domain.

ii. MHC Binding Peptides, and MHC Binding Peptide Libraries/Pools

An MHC-binding peptide (e.g., an antigenic peptide or T cell epitope) ofthe present invention can comprise any peptide that is capable ofbinding to an MHC protein. In preferred embodiments, the peptide bindsto an MHC protein in a manner such that the peptide-MHC complex can bindto a TCR. In further preferred embodiments, the peptide-MHC complex,upon binding to a TCR, induces a T cell response. The MHC bindingpeptide of the present invention can be an MHC class I binding peptideand/or an MHC class II binding peptide. An MHC class I binding peptidecan be a polypeptide which is capable of selectively binding within thebinding cleft formed by a specified MHC class I molecule to form a classI MHC-peptide complex. An MHC class I binding peptide is typically 8-10amino acid residues in length, and may be longer or shorter and stilleffective. An MHC class II binding peptide can be a polypeptide which iscapable of selectively binding within the binding cleft formed by the αand β chains of a specified MHC class II molecule to form a class IIMHC-peptide complex. An MHC class II binding peptide is typically 10-25,and more typically 13-18, amino acid residues in length, and may belonger or shorter and still effective. In certain embodiments, anMHC-binding peptide (including an MHC class I binding peptide and an MHCclass II binding peptide) may be a self or non-self peptide, or asynthetic peptide. In certain aspects, an MHC binding peptide can beprocessed, for example, by an antigen presenting cell (APC). In otheraspects, an MHC binding peptide is not processed by a cell beforecontacting an MHC molecule of the present invention.

Provided herein are candidate MHC-binding peptides, each produced to bea candidate for binding to an MHC molecule and/or binding to a TCR. Assuch, a “candidate MHC-binding peptide,” a “candidate antigenic peptide”and an “MHC-binding peptide” can be used interchangeably. An MHC-bindingpeptide that binds to an MHC molecule and is recognized, in conjunctionwith the MHC molecule, by a TCR, is considered to be an antigenicpeptide.

In cells, class I MHC proteins typically present antigenic peptidesderived from proteins actively synthesized in the cytoplasm of the cell.In contrast, class II MHC proteins typically present antigenic peptidesderived either from exogenous proteins that enter a cell's endocyticpathway or from proteins synthesized in the ER. Intracellulartrafficking permits an antigenic peptide to become associated with anMHC protein. The resulting MHC-peptide complex then travels to thesurface of the cell where it is available for interaction with a TCR.Candidate MHC-binding peptides of the present invention, however, can begenerated or obtained by any suitable methods known to one of skill inthe art. In certain embodiments, the candidate MHC-binding peptides canbe peptides produced by hydrolysis. In other embodiments, the candidateMHC-binding peptides are synthetically produced peptides, includingrandomly generated peptides, specifically designed peptides, andpeptides where at least some of the amino acid positions are conservedamong several peptides and the remaining positions are random.

The binding of a peptide to an MHC peptide binding groove can controlthe spatial arrangement of MHC and/or peptide amino acid residuesrecognized by a TCR. Upon identification of MHC binding peptides usingmethods of the present invention, how peptides bind to the MHC moleculecan be determined. For example, the major MHC anchor amino acids of apeptide which are typically held constant can be determined. In anotheraspect, the surface exposed amino acids that are varied among differentpeptides can be determined. In one embodiment, the length of anMHC-binding peptide is from about 5 to about 40 amino acid residues,preferably from about 6 to about 30 amino acid residues, and morepreferably from about 8 to about 20 amino acid residues, and even morepreferably between about 9 and 11 amino acid residues, including anysize peptide between 5 and 40 amino acids in length, in whole integerincrements (i.e., 5, 6, 7, 8, 9 . . . 40). While naturally MHC classII-bound peptides vary from about 9-40 amino acids, in nearly all casesthe peptide can be truncated to an about 9-11 amino acid core withoutloss of MHC binding activity or T cell recognition. Without being boundby any theory, the MHC binding peptides of the present inventionencompass peptides disclosed in any embodiments of the present inventionor any combination thereof

Peptides used in the invention can include peptides comprising at leasta portion of an antigen selected from a group consisting ofautoantigens, infectious agents, toxins, allergens, or mixtures thereof.However, one aspect of the invention is the use of syntheticallyproduced peptides to identify the peptides bound to a particular MHC ata spectrum of specificities and/or affinities, and to identify theantigens recognized by a specific T cell at a spectrum of specificitiesand/or affinities. Therefore, preferred peptides are from libraries ofsynthetically produced peptides, including, but not limited to, peptidelibraries produced by PCR (including by introducing random mutationsinto various positions of a template peptide). A peptide library (usedherein interchangeably with “peptide pool”) can include at least 2, andup to about 5, about 10, about 20, about 30, about 40, about 50, about60, about 70, about 80, and about 90 member peptides. In otherembodiments, a peptide library includes up to about 1×10², about 2×10²,about 3×10², about 4×10², about 5×10², about 6×10², about 7×10², about8×10², about 9×10², about 1×10³, about 2×10³, about 3×10³, about 4×10³,about 5×10³, about 6×10³, about 7×10³, about 8×10³, about 9×10³, andabout 1×10⁴ member peptides. Without being bound by any theory, apeptide library of the present invention can include up to about 1×10⁴,about 2×10⁴, about 3×10⁴, about 4×10⁴, about 5×10⁴, about 6×10⁴, about7×10⁴, about 8×10⁴, about 9×10⁴, or about 1×10⁵ member peptides. Incertain embodiments, a peptide library of the present can include morethan about 1×10⁵ member peptides. In some cases, T cell recognition isdominated by only a few amino acids in the core of the peptide, and inthese cases, libraries with only a few hundred to a few thousand membersare sufficient to identify functional peptide-MHC complexes.

Extensive knowledge regarding the binding of peptides to MHC complexesis available to the public, so that for a given MHC complex, one candesign MHC-groove binding peptides that vary in less than all of theavailable positions. For example, the MHCBN is a comprehensive databaseof Major Histocompatibility Complex (MHC) binding and non-bindingpeptides compiled from published literature and existing databases. Thedatabase has sequence and structure data of (a) source proteins ofpeptides and (b) MHC molecules. MHCBN has a number of web tools thatinclude: (i) mapping of peptide on query sequence; (ii) search on anyfield; (iii) creation of data sets; and (iv) online data submission(Bhasin et al., 2003, Bioinformatics 19(5): 665-666). In certainembodiments, the MHCBN is used to design a complex set of peptide-cDNAconjugates (or other peptide-polynucleotide conjugates) of the presentinvention. In preferred embodiments, the Immune Epitope Database (IEDB)is used to design a complex set of peptide-cDNA conjugates (e.g. >200)with known binding across all listed human HLA molecules. Bindingstudies for 207 human class II HLA molecules are listed in the IEDB.This set of “eigenpeptides” can be selected so that each member binds asnarrow a set of HLA molecules as possible, thus providing both range andspecificity (illustrated in FIG. 2). This peptide set can be testedagainst HLA class II molecules isolated from peripheral bloodmononuclear cells (PBMCs) from healthy donors of known HLA types. Thisanalysis allows the identification of a panel of reference peptides withbinding across many HLA genotypes, which then serves as a usefulinternal normalization set for studies using peptide sets of highercomplexity.

In one embodiment of the invention, the MHC-binding peptide is from alibrary of candidate antigenic peptides, wherein the each of thepeptides in the library comprises conserved amino acids in a specificsequence sufficient to enable the peptide to bind to the peptide bindinggroove of an MHC molecule. In a more specific embodiment, theMHC-binding peptide is from a library of candidate antigenic peptides,wherein each of the peptides in the library comprises between about 4and 5 conserved amino acids in a specific sequence sufficient to enablethe peptide to bind to the peptide binding groove of an MHC molecule.

In one embodiment, a library of candidate peptides (candidate antigenicpeptides or MHC-binding peptides) is produced by genetically engineeringthe library using polymerase chain reaction (PCR) or any other suitabletechnique to construct a DNA fragment encoding the peptide. With PCRtechniques, by using oligonucleotides that are randomly mutated withinparticular triplet codons, the resultant fragment pool encodes allpossible combination of codons at these positions. Preferably, certainof the amino acid positions are maintained constant, which are theconserved amino acids that are required for binding to the MHC peptidebinding groove and which do not contact the T cell receptor.

iii. Implications of MHC and MHC Binding Peptides in Diseases

Peptide-MHC binding is generally related to immune activity and/orinactivity, and thereby has implications in a wide range of conditionsand diseases, including but not limited to inflammation, allergy,autoimmune diseases, various types of cancers, and infection (viral orbacterial). Patients with diseases associated with immunosuppression,such as cancer, may benefit from strategies to remove immunosuppressionand/or enhance tumor-specific immune response. In one aspect, the canceris a cancer of the adrenal gland, bladder, bone, bone marrow, brain,breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart,kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis,prostate, salivary glands, skin, spleen, testis, thymus, thyroid, oruterus. On the contrary, patients with diseases associated withheightened immune activity, such as inflammation, autoimmunity, allergy,and asthma, may benefit from strategies to down-regulate immuneresponses. In certain embodiments, the autoimmune disease is Addison'sDisease, autoimmune hemolytic anemia, autoimmune inner ear disease,autoimmune lymphoproliferative syndrome, autoimmune thrombocytopenicpurpura, autoimmune hemolytic anemia, autoimmune hepatitis, autoimmuneoophoritis, Behçet's disease, autoimmune bullous pemphigoid, autoimmunecardiomyopathy, Crohn's disease, autoimmune chronic fatigue syndrome,chronic obstructive pulmonary disease (COPD), including chronicbronchitis, emphysema and chronic asthmatic bronchitis, autoimmunedermatomyositis, autoimmune diabetes mellitus type-1, autoimmuneepilepsy autoimmune, Kawasaki's disease, autoimmune glomerulonephritis,Grave's disease, Goodpasture's syndrome, Guillain-Barré syndrome, lupusnephritis, multiple sclerosis, myasthenia gravis, autoimmunemyocarditis, autoimmune Parkinson diseases, pediatrics autoimmuneneuropsychiatry disorders, autoimmune pemphigus/pemphigoid, autoimmunepernicious anemia, autoimmune polyarteritis nodosa, autoimmunepolymyositis, autoimmune primary biliary cirrhosis, psoriasis,autoimmune rheumatic fever, rheumatoid arthritis, autoimmunesarcoidosis, scleroderma, Sjogren's syndrome, autoimmune thyroiditis,autoimmune ulcerative colitis, autoimmune uveitis, autoimmune vitiligo,Wegener's granulomatosis, or Wilson's disease.

The peptides identified using methods of the present invention may havesignificantly lower, lower, the same, about the same, higher, orsignificantly higher binding affinities and/or specificities to an MHCmolecule, when compared to a reference. The reference can be a bindingaffinity and/or specificity to a particular MHC molecule detected in acontrol normal subject, or in a control normal tissue or cell of apatient, or in a population of such control normal subjects or controlnormal tissues or cells. Depending on the needs of a patient, thepeptides identified using methods of the present invention may be usedto enhance, suppress, or regulate immune response in the patient.

The importance of the peptide-MHC complex in determining immune outcomesis also demonstrated by the large and increasing number of humangenome-wide association studies that have strongly linked the genomicHLA locus to outcomes as diverse as autoimmunity (Wong and Wen, 2003,Curr. Mol. Med. 3: 1-15; Fernando et al., 2008, PLoS Genet. 4: e1000024;Handunnetthi et al., 2010, Genes Immun. 11: 99-112), allergy (Marsh etal., 1973, Science 179: 691-693; Moffatt et al., 2010, N. Engl. J. Med.363: 1211-1221), susceptibility to infection (International HIVControllers Study, 2010, Science 330: 1551-1557) and drug reaction (Dalyet al., 2009, Nat Genet. 41: 816-819; Chung et al., 2004, Nature 428:486; Hung, 2005, Proc. Natl. Acad. Sci. U S A. 102: 4134-4139).Particular alleles of the MHC have been associated with a variety ofdiseases, including autoimmune diseases such as multiple sclerosis (MS),rheumatoid arthritis (RA), pemphigus vulgaris (PV), and systemic lupuserythematosus (SLE). It has been suggested that particular MHC proteins“improperly” recognize processed self peptides presented to T cells inthe form of complexes with MHC Class I or Class II molecules. Forexample, susceptibility of MS is associated with the MHC class IIregion, and particular MHC class II haplotypes confer an increased riskof MS. The strongest association is with the HLA-DR2 haplotype(DRB1*1501). HLA-DR2 (encoded by the DRA, DRB 1*1501 genes) has beenshown to present at least two peptides of human myelin basic protein(residues 85-99 and 148-162) to T cells. The MBP(85-99) peptide bindswith high affinity to purified DR2, and the affinity of the MBP(148-162)peptide is lower but significant.

Underlying these associations is the fact that inter-individualvariation in the HLA is extreme: each HLA haplotype encodes 3 class Iand 3 class II complexes, these haplotypes are co-dominantly expressedand represent the most polymorphic loci in the genome. In total, thisvariation results in >104 different possible HLA class I and IImolecules, ˜12 of which will occur in any given individual. Thiscomplexity provides broad protection at the population level, ensuringthat at least some members of the population have the capacity topresent antigens from a given pathogen threat. However, a corollary isthat there exists substantial inter-individual heterogeneity in thespectrum of antigen peptides that can be presented to T cells, resultingin a corresponding heterogeneity in immune responses. Addressing thisheterogeneity is a key objective of personalized medicine and thepresent invention.

Since the present invention provides methods for understanding whichpeptides are recognized by a given MHC molecule, and which peptides arepresented by a subject to elicit an immune response, one of skill in theart would appreciate that the methods disclosed herein are useful for avariety of purposes, including: (a) to identify peptide epitopes for thepurpose of vaccine design; (b) to enable identification and monitoringof specific T cell responses against viruses, autoantigens, allergens;(c) to identify novel antigens in infection, autoimmunity, allergy, orcancer; (d) to test the potential immunogenicity of protein-basedtherapeutics.

C. Polynucleotide-Peptide Conjugates

The polynucleotide-peptide conjugate of the invention includes anoligonucleotide or a polynucleotide, used herein interchangeably, whichmay be a part of a larger nucleotide construct such as a plasmid. Incertain embodiments, the polynucleotide can be an oligonucleotide, amodified oligonucleotide and oligonucleoside, alone or as part of alarger construct. The polynucleotide may be single-stranded DNA (ssDNA),double-stranded DNA (dsDNA), single-stranded RNA (ssRNA) ordouble-stranded RNA (dsRNA). In one aspect, the polynucleotide portioncan be linearly or circularly configured, or the oligonucleotide portioncan contain both linear and circular segments. Modifications ofoligonucleotides include, but are not limited to, modifications of the3′OH or 5′OH group, modifications of the nucleotide base, modificationsof the sugar component, and modifications of the phosphate group.

The polynucleotide of the polynucleotide-peptide conjugate of theinvention may comprise ribonucleotides (containing ribose as the only orprincipal sugar component), deoxyribonucleotides (deoxyribose as theprincipal sugar component), or in accordance with establishedstate-of-the-art modified sugars or sugar analogs may be incorporated inthe oligonucleotide of the present invention. Thus, in addition toribose and deoxyribose, the sugar moiety may be pentose, deoxypentose,hexose, deoxyhexose, glucose, arabinose, xylose, lyxose, and a sugar“analog” cyclopentyl group. The sugar may be in pyranosyl or in afuranosyl form. The preparation of these sugars or sugar analogs and therespective “nucleosides” wherein such sugars or analogs are attached toa heterocyclic base (nucleic acid base) per se is known.

The phosphorous derivative (or modified phosphate group) which may beattached to the sugar or sugar analog moiety in the modifiedoligonucleotides of the present invention may be a monophosphate,diphosphate, triphosphate, alkylphosphate, alkanephosphate,phosphorothioate, phosphorodithioate or the like. The preparation of theabove-noted phosphate analogs, and their incorporation into nucleotides,modified nucleotides and oligonucleotides, per se, is also known.

The heterocyclic bases, or nucleic acid bases which are incorporated inthe oligonucleotide base of the polynucleotide-peptide conjugate of theinvention may be the naturally occurring principal purine and pyrimidinebases, (namely uracil or thymine, cytosine, adenine and guanine, asmentioned above), as well as naturally occurring and syntheticmodifications of said principal bases. Those skilled in the art willrecognize that a large number of “synthetic” non-natural nucleosidescomprising various heterocyclic bases and various sugar moieties (andsugar analogs) have become available in the art.

Without being bound by any theory, the probe that specifically binds tothe polynucleotide of the polynucleotide-peptide conjugate of theinvention may also be any natural or modified polynucleotide orderivative as described in any embodiments disclosed herein or anycombinations thereof

A variety of methods can be used to conjugate a polynucleotide to acandidate MHC-binding peptide. For example, as described in Example 1,peptide-cDNA conjugates can be produced from DNA molecules by eitherCoA-mediated formation or puromycin-mediated formation. Each method canbe implemented at high plexity, for example by using high-complexitymicroarrays as a source of DNA templates. To this end, one approach isby multimerization or oligomerization of the polynucleotide-peptideconjugate. Any methods known to one of skill in the art as suitable forthe present invention can be used. For example, as described in Example2, multivalent peptide-cDNA conjugate molecules can be obtained throughmultimerization mediated by multivalent adapters, or multimerizationthrough hybridization of the polynucleotides. These approaches formultimerization of polynucleotide-peptide conjugates can also beimplemented in conjunction with each other to enable even higher ordermultiplexing.

In another embodiment, an inexpensive parallel oligonucleotide synthesismethod is used. A large pool of in silico-designed DNA templates aresynthesized, each containing a T7 promoter, ribosomal binding site,sequences coding for N- and C-terminal peptide tags, and a variableregion coding for custom peptide sequences. These oligonucleotides arethen transcribed and translated in vitro, using a process in which eachtranslated peptide becomes covalently coupled to its encoding RNA, whichis subsequently reverse-transcribed into cDNA. A schematic overview ofthe pool production process illustrating its intrinsically parallel andscalable nature is shown in FIG. 3A. The production of pools of severalthousand peptide-cDNA conjugates tiling through the Hepatitis C Virus(HCV) polyprotein and their utility in assaying the activity of HCVNS3/4A protease are shown in FIG. 3B and described in more detail inShiryaev et al, 2012, PLoS ONE 7(4): e35759.

In preferred embodiments, the polynucleotide-peptide conjugate of thepresent invention is not associated, complexed, or conjugated with, orotherwise immobilized to any surface, membrane, or the like beforecontacting an MHC molecule. For example, in one aspect, thepolynucleotide-peptide conjugate of the present invention, including amultimerized or oligomerized conjugate, is not associated, complexed, orconjugated with a cellular membrane or a viral particle. In oneembodiment, the polynucleotide-peptide conjugate disclosed herein is notassociated, complexed, or conjugated with a phage coat protein.

D. Methods of Detecting Peptide Binding to an MHC Molecule

Provided here are also methods for detecting binding of a candidateMHC-binding peptide to an MHC molecule. In preferred embodiments,detection of competitive binding of a pool or library of multiplecandidate MHC-binding peptides to a particular MHC molecule isaccomplished by the present invention. In one embodiment, a scalable,multiplexed, competition-based binding assay capable of testing large,customizable peptide sets across all of an individual's HLA class IImolecules, is provided. For a given MHC molecule, the ability to detectbinding of multiple candidate MHC-binding peptides at the same time, andto compare their relative binding affinity and/or specificity to the MHCmolecule, makes the present invention particularly useful for thediagnosis, treatment, and/or prognosis of human diseases.

In one embodiment, a method for detecting binding of a peptide to an MHCmolecule is disclosed. The method comprises: contacting said MHCmolecule with a polynucleotide-peptide conjugate, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide; contacting said polynucleotide-peptide conjugate with aprobe that specifically binds to said polynucleotide; detecting bindingof said probe to said polynucleotide; and, correlating binding of saidprobe to said polynucleotide with binding of said peptide to said MHCmolecule.

In another embodiment, a method for simultaneously detecting binding ofa library of peptides to an MHC molecule is provided. The methodcomprises: providing a polynucleotide-peptide conjugate for each saidpeptide, said polynucleotide-peptide conjugate comprising said peptideand a polynucleotide; contacting said MHC molecule with a pool of saidpolynucleotide-peptide conjugates; contacting each of saidpolynucleotide-peptide conjugate with a probe that specifically binds toeach said polynucleotide; detecting binding of said probe to eachcorresponding polynucleotide that each said probe specifically binds;and correlating binding of said probe to each correspondingpolynucleotide with binding of each corresponding peptide to said MHCmolecule. In another embodiment, the method further comprises comparingbinding of each said peptide to said MHC molecule, among the peptides insaid library.

In yet another embodiment, provided herein is a method for detecting ina library of peptides competitive binding of each said peptide to an MHCmolecule, comprising: providing a polynucleotide-peptide conjugate foreach said peptide, said polynucleotide-peptide conjugate comprising saidpeptide and a polynucleotide; contacting said MHC molecule with a poolof said polynucleotide-peptide conjugates; contacting each of saidpolynucleotide-peptide conjugate with a probe that specifically binds toeach said polynucleotide; detecting binding of said probe to eachcorresponding polynucleotide that each said probe specifically binds;and correlating binding of said probe to each correspondingpolynucleotide with binding of each corresponding peptide to said MHCmolecule, wherein said peptides compete for binding of said MHCmolecule. In another embodiment, the method further comprises comparingbinding of each said peptide to said MHC molecule, among the peptides insaid library.

In one embodiment, the method disclosed herein is used in a multiplexedpeptide-MHC binding assay. As shown in FIG. 1 (upper panel), MHCmolecules are tested in a pooled binding reaction against a set of insilico-programmed peptide-cDNA conjugates. Bound peptides are identifiedby high throughput DNA sequencing, which has the dynamic range to revealthe spectrum of differentially-competitive MHC binders.

In any of the foregoing method embodiments or any combination thereof,an MHC molecule can be contacted with a polynucleotide-peptide conjugatefirst, followed by washing away of unbound conjugate, and then theMHC-conjugate complex is contacted with a probe specific for thepolynucleotide. In another embodiment, a polynucleotide-peptideconjugate can be contacted with a probe first, before the mixture iscontacted with an MHC molecule. In yet another embodiment, an MHCmolecule can be contacted with a polynucleotide-peptide conjugate and aprobe at about the same time, and the polynucleotide-peptide conjugatedoes not need to contact the probe first.

In one embodiment, the MHC molecule is immobilized to a carrier. Thecarrier can be a molecule, particle, composition, or other microscopicobject to which may be conjugated, directly or indirectly, at least oneMHC molecule, and in preferred embodiments, a multiplicity of MHCmolecules. In certain embodiments, the carrier refers to the backbone ofthe conjugate, on which various molecules may be attached. In particularexamples, the carrier comprises water-soluble polymers, including butare not limited to natural and synthetic polysaccharides, as well asderivatives thereof, for example dextrans and dextran derivatives,starches and starch derivatives, cellulose derivatives, amylose andpectin, as well as certain natural gums and derivatives thereof, such asgum arabic and salts of alginic acid; homopoly(amino acid)s havingsuitable reactive functionalities, such as polylysines, polyhistidinesor polyornithines; natural and synthetic polypeptides and proteins, suchas bovine serum albumin, immunoglobulins, and other mammalian albumins;and synthetic polymers having nucleophilic functional groups, such aspolyvinyl alcohols, polyallyl alcohol, polyethylene glycols andsubstituted polyacrylates.

In certain embodiments, the carrier is a molecule. In other embodiments,the carrier is a surface. The surface can be a plastic surface, or asurface comprised in a nitrocellulose membrane, a nylon membrane, alatex particle, or a gold particle. In certain embodiments, the MHCmolecule is biotinylated and the carrier is modified with streptavidin.The MHC molecule and the carrier can be otherwise modified for use inthe present invention.

In some embodiments, the carrier is biodegradable, the carrier isnon-immunogenic, the carrier has a net neutral or negative charge,and/or the carrier is fluorescently labeled. The carrier may becovalently or non-covalently bound to a surface, such as a plasticsurface, or a surface comprised in a nitrocellulose membrane, a nylonmembrane, a latex particle, or a gold particle. In some embodiments, thecarrier is a substantially spherical bead or a porous bead. In certainembodiments in which the carrier is a bead, the bead preferablycomprises a material selected from the group consisting of glass,silica, polyesters of hydroxy carboxylic acids, polyanhydrides ofdicarboxylic acids, or copolymers of hydroxy carboxylic acids anddicarboxylic acids. In some embodiments, the carrier is a branchedpolymer, such as a dendrimer. In preferred embodiments when the carrieris a dendrimer, the dendrimer comprises a material selected from thegroup consisting of a polyamidoamine, a polyamidoalcohol, apolyalkyleneimine, a polyalkylene, a polyether, a polythioether, apolyphosphonium, a polysiloxane, a polyamide, and a polyaryl polymer.

In some embodiments, the MHC molecule/carrier complex further comprisesa linker. A linker can be a bi-functional molecule capable ofestablishing covalent links between other molecules. Examples ofbi-functional molecules suitable as linkers include but are not limitedto glutaraldehyde, carbodiimides, N,N′-phenylenedimaleimide,N-succinimidyl 3-(2-pyridylthio)propionate, p-benzoquinone, divinylsulfone (DVS) and epoxide derivatives such as epichlorohydrin and otherepoxide derivatives described in U.S. Pat. No. 6,627,460, incorporatedherein by reference. Preferably, the linking component should be stablein an aqueous environment. In some embodiments, the MHC molecule/carriercomplex further comprises a spacer. A spacer can be a protein or apolypeptide having a plurality of sites available for covalentattachment of other components. Although not necessary for practicingthe invention, a spacer may provide a suitable means of increasing thenumber of cobinamide moieties which can be attached to the conjugate,thereby increasing the sensitivity of such conjugates when employed invarious assays. Examples of protein spacers include but are not limitedto bovine serum albumin, ovalbumin, globulin, etc. Examples ofpolypeptide spacers include but are not limited to homopolypeptides,such as polylysines, polyhistidines, polyornithines, etc. As will beclear to a person skilled in the art, the choice of spacer will dependon the employed MHC molecule, the employed carrier, as well as theemployed linking component. In some aspects, the spacer component can bea polysaccharide or polynucleic acid. Chemical modifications of thesepolymers may be required prior to the preparation of the water-solubleintermediate conjugate.

In a preferred embodiment, the pools of peptides bearing uniquepolynucleotide tags (e.g., DNA-tags) allow many peptides to be testedfor binding in a single reaction and reported by high throughputsequencing. Advantages of the present polynucleotide-conjugate basedassay approach include:

(a) Defined content. Bioinformatically-defined oligonucleotide sequencesof choice are produced by parallel synthesis on an array, and thenconverted into the corresponding cDNA-peptide conjugates. The system canbe readily programmed to display peptides from any immunogen of choice.For example, the present inventors have already synthesized andvalidated in protease assays sets of peptide-cDNA conjugates that tilethrough the 3,011 amino acid HCV proteome with a step resolution of 1amino acid (Kozlov et al., 2012, PLoS One 7: e37441).

(b) Intrinsic, competition-based multiplexing. The proteolytic processesof the proteasome (for class I) and endosome (for class II) give rise tocomplex peptide milieus, and the present inventors have utilized thepeptide-peptide competition for MHC binding. In one embodiment, thepresent invention provides a biologically relevant way to increase theplexity of a peptide-MHC binding assay by a solution-phase approach,where inter-peptide competition is possible, rather than an immobilizedpeptide approach. In one aspect, the present invention provides methodsto narrow a large number of peptides found to bind an MHC molecule, forexample, those in published peptide microarray studies (Gaseitsiwe etal., 2009, Clin Vaccine Immunol. 16: 567-573; Gaseitsiwe et al., 2010,Clin Vaccine Immunol. 17: 168-175), to the best binders.

(c) Next generation sequencing readout. Among other advantages, nextgeneration sequencing has high sensitivity, allowing binders to bedetected among large peptide pools.

In one embodiment, peptide-cDNA conjugates are used as multiplex probesfor MHC binding. For example, in Example 3, the MHC class II moleculesHLA-DR3 and HLA-DR1 were biotinylated and immobilized on streptavidinbeads, and two peptides known to bind HLA-DR3 and HLA-DR1, respectively,without cross-binding, were used to bind the MHC class II molecules. Thepeptide-cDNA conjugates comprising the two peptides were detected by gelelectrophoresis and quantitative polymerase chain reaction for thepolynucleotide portions of the conjugates. The results indicate thateach conjugate bound to the expected MHC molecule but not to the otherHLA-DR family member. In another example, three peptides known to bindthe HLA-DR1 molecule with high, high, and low affinities, respectively,were used. The results indicate the expected profile of binding for thethree conjugates (high, high, low), both in the case where conjugateswere present individually (1-plex), and in the case where the conjugateswere incubated and detected as a mixture (3-plex).

In one embodiment, multiplexing of the peptide-MHC binding assay acrossmultiple peptides is performed using the next-generation sequencingreadout. For example, 45 candidate peptides can be chosen from theproteome of influenza A virus on the basis that they are conservedacross different strains and predicted to bind the majority of commonHLA-DR molecules. Peptide-cDNA-conjugates corresponding to these 45sequences can be prepared and incubated with recombinant biotinylatedHLA-DR3. In this example, HLA-DR3 is selected as a representative HLAmolecule because it is one to which binding of the 45 peptides has beenmeasured, with a wide range of binding affinities for the differentpeptides. Without being bound by any theory, other MHC molecules may beused. The reported binding affinities of the 45 peptides to the MHCmolecule can be used as reference. In one embodiment, the signalsobtained for these 45 peptides in multiplex and single-plex assays arecompared with their reported binding affinities. In one aspect, themethod of the present invention provides a comprehensive data matrixthat includes known positives and negatives, serving as an ideal systemto test and optimize new assay format.

In preferred embodiments, the method disclosed herein iscompetition-based. In preferred embodiments, the method disclosed hereinuses a sequencing readout. As such, in certain embodiments, the type ofdata generated by methods of the invention differs considerably fromwhat has been generated in single-plex binding experiments, or evenpeptide microarray experiments. In one embodiment, the multiplexedcompetitive binding format manifests as a strongly skewed representationof the starting peptides according to their binding affinity. As well asallowing the best binders to be identified from the pool, in certainaspects, lower affinity binders are discriminated from non-binders, forexample, thanks to the high sensitivity and large dynamic range of nextgeneration sequencing. In preferred embodiments, lower affinity bindersare discriminated from non-binders, and simultaneously the best bindersare also identified from the pool. In one embodiment, the methodsdisclosed herein are used in conjunction with previously reportedaffinities, for example, to develop analysis approaches that can relatesequence abundance with binding affinity.

In one embodiment, peptide-MHC binding assays to HLA sets isolated fromhuman samples, for example, human blood samples, are performed. Inanother embodiment, peptide-MHC binding assays are performed to identifypersonalized pathogen epitopes. In one aspect, a multiplexed peptide-MHCbinding assay method is used for defined recombinant HLA molecules. Inanother aspect, a multiplexed peptide-MHC binding assay method is usedfor bulk genotype-based sets of HLA molecules isolated from human blood.Protocols for the isolation of HLA molecules from primary human cellsare established (Fissolo et al., 2009, Mol. Cell Proteomics. 8:2090-2101), however the preference for transfected cells or cell linesas sources of HLA molecules reflects the fact that traditional assayformats require large quantities of single HLA species. In contrast, fora multiplexed assay read-out by sensitive next generation sequencing,there is no need to isolate single MHC-peptide pairs. In a preferredembodiment, the method disclosed herein does not require isolation ofsingle MHC-peptide pairs. In one embodiment, the method disclosed hereinis sensitive and requires significantly less HLA material. In oneexample, the binding of peptide-cDNA conjugates to sets of HLA class IImolecules derived from the peripheral blood mononuclear cells (PBMCs) ofanonymous human donors is detected. PBMCs represent a readily-availablebiological sample type, and one in which HLA class II proteins areabundantly expressed. In certain aspects, the method comprises: (a)incubating polynucleotide-peptide conjugates with cells; lysing cells;immunoprecipitating HLA molecules; eluting the conjugates; or (b) lysingcells; immunoprecipitating HLA molecules; incubatingpolynucleotide-peptide conjugates with cells; eluting the conjugates; or(c) incubating polynucleotide-peptide conjugates with cells; elutingpeptides from cells directly. In one aspect, the 45 influenza encodedpeptides described above for binding to the HLA molecules of 10influenza reactive human donors are used. In one embodiment, a snapshotof the influenza:HLA class II “presentome” for each of the donorindividuals are provided. In some embodiments, such a snapshot can be aprofile of which peptides can be presented by which donor but not byothers. In some embodiments, the binding profiles are then compared withtwo orthogonal sources of information about the donors' influenzaepitopes: (i) T cell reactivity profiles of the 10 donors for the same45-peptide set, generated using the traditional ELISpot assay, and (ii)the HLA genotypes of the 10 donors, crossmatched with the publishedbinding affinities of the peptides for 17 individual HLA-DR molecules.

In one aspect, an application of the peptide-MHC binding assaysdisclosed herein is the prediction of epitopes that are recognized by Tcells during an immune response, in particular, during a T cellresponse. Although the ability to interact with MHC is one of severalfactors necessary for a peptide to generate a T cell response (other keyfactors being proteolytic production of the peptide, and availability ofbinding T cells within the T cell repertoire), there is evidence thatMHC interaction has a large effect and can be powerfully predictive.

At equilibrium, biomolecular binding is a function of both association(the rate at which the molecules become bound with each other) anddissociation (the rate at which the molecules detach from each other).In some aspects, binding assays report how much binding is present atequilibrium (a convolution of both association and dissociation). Inother aspects, however, slow dissociation of a particular peptide-MHCcomplex is an independent and key requirement for a peptide to elicit aT cell response. See for example, Yin et al., “HLA-DM constrains epitopeselection in the human CD4 T cell response to vaccinia virus by favoringthe presentation of peptides with longer HLA-DM-mediated half-lives,” JImmunol. 2012, 189: 3983-94. See also Lazarski et al., “The kineticstability of MHC class II:peptide complexes is a key parameter thatdictates immunodominance,” Immunity. 2005, 23: 29-40. The disclosures ofthese references are incorporated herein by reference in theirentireties for all purposes.

In one aspect, disclosed herein is a method of detecting specificbinding of a polypeptide to an MHC molecule, comprising setting up anequilibrium between a polynucleotide-peptide conjugate (thepeptide-bearing probe) and the MHC molecules, washing away unboundpolynucleotide-peptide conjugate molecules, and leaving the loaded MHCcomplexes to dissociate for a period of time (e.g., ≥about 30 minutes, 1hour, 2 hours, 3 hour, 4 hours, 5 hour, 6 hours, 7 hour, 8 hours, 9hour, 10 hours, 11 hour, 12 hours, 13 hours, 14 hours, 15 hours, orabout 16 hours), optionally in the presence of one or more blockerspecies that binds MHC but does not generate signal, and then assayingthe polynucleotide-peptide conjugates that remain bound to the MHCmolecules. In one embodiment, the one or more blocker species competewith the peptide moieties of the polynucleotide-peptide conjugates inbinding to the MHC molecules, thereby preventing peptide reassociatingwith the MHC molecule.

In any of the embodiments disclosed herein, chemical chaperones can beadded before, during, or after allowing the polynucleotide-peptideconjugates to bind to the MHC molecules. In one aspect, physiologicalpeptide-MHC binding occurs in the presence of a protein chaperone (e.g.,HLA-DM) that facilitates peptide loading and unloading onto MHCmolecules and acts to shape the repertoire of peptides that bind MHC andare responded to by T cells. In one aspect, the biological utility ofthe multiplexed peptide:MHC assay disclosed herein can be improved bythe addition of chaperones that recapitulate this function, such asrecombinant HLA-DM and small molecule chaperones that have the same orsimilar effects. These include parachlorophenol (pCP) ordimethylsulphoxide (DMSO). See Marin-Esteban et al., J Biol Chem. 2004,279: 50684-90, which discloses that chemical analogues of HLA-DM caninduce a peptide-receptive state in HLA-DR molecules. The disclosure ofMarin-Esteban et al. is incorporated herein by reference in its entiretyfor all purposes.

E. Methods of Detecting Peptide Binding to a TCR or a T Cell

Provided here are also methods for detecting binding of a candidateMHC-binding peptide to a TCR or a T cell. In preferred embodiments,detection of competitive binding of a pool or library of multiplecandidate MHC-binding peptides to a particular MHC molecule/TCRcombination is accomplished by the present invention. In one embodiment,a polynucleotide-peptide conjugate (e.g., peptide-cDNA conjugate) isbound to MHC molecules as probes for the multiplexed detection ofspecific T cells. In one aspect, the polynucleotide-peptide conjugate ismultimerized or oligomerized.

In one aspect, disclosed herein is a method for detecting binding of apeptide to a T cell, comprising: contacting said T cell with an MHCmolecule an a polynucleotide-peptide conjugate, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide; contacting said polynucleotide-peptide conjugate with aprobe that specifically binds to said polynucleotide; detecting bindingof said probe to said polynucleotide; and, correlating binding of saidprobe to said polynucleotide with binding of said peptide to said Tcell.

In another aspect, a method for simultaneously detecting binding of alibrary of peptides to a T cell is provided. This method comprises:providing a polynucleotide-peptide conjugate for each said peptide, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide; contacting said T cell with a pool of saidpolynucleotide-peptide conjugates and an MHC molecule; contacting eachof said polynucleotide-peptide conjugate with a probe that specificallybinds to each said polynucleotide; detecting binding of said probe toeach corresponding polynucleotide that each said probe specificallybinds; and correlating binding of said probe to each correspondingpolynucleotide with binding of each corresponding peptide to said Tcell. In one embodiment, the peptide of the present invention binds aTCR of said T cell.

In yet another aspect, described herein is a method for detecting in alibrary of peptides competitive binding of each said peptide to a Tcell, comprising: providing a polynucleotide-peptide conjugate for eachsaid peptide, said polynucleotide-peptide conjugate comprising saidpeptide and a polynucleotide; contacting said T cell with a pool of saidpolynucleotide-peptide conjugates and an MHC molecule; contacting eachof said polynucleotide-peptide conjugate with a probe that specificallybinds to each said polynucleotide; detecting binding of said probe toeach corresponding polynucleotide that each said probe specificallybinds; and correlating binding of said probe to each correspondingpolynucleotide with binding of each corresponding peptide to said Tcell, wherein said peptides compete for binding of said MHC molecule andsaid T cell. In one embodiment, the peptide binds a TCR of said T cell.

In any of the embodiments disclosed herein or any combination thereof,the method of the present invention can further comprise comparing thedetected binding of said peptide to said MHC molecule or said T cellwith a reference. In a further embodiment, the method of the presentinvention as disclosed in any embodiments or any combination thereoffurther comprises selecting the detected binding of said peptide overthe reference, for the purposes of identifying antigens in infection,autoimmunity, allergy, or cancer, or for vaccine design.

In any of the foregoing method embodiments or any combination thereof,an MHC/TCR pair can be contacted with a polynucleotide-peptide conjugatefirst, followed by washing away of unbound conjugate, and then theMHC-TCR-conjugate complex is contacted with a probe specific for thepolynucleotide. In another embodiment, a polynucleotide-peptideconjugate can be contacted with a probe first, before the mixture iscontacted with an MHC/TCR pair. In yet another embodiment, an MHC/TCRpair can be contacted with a polynucleotide-peptide conjugate and aprobe at about the same time, and the polynucleotide-peptide conjugatedoes not need to contact the probe first.

In any of the embodiments disclosed herein or any combination thereof,the polynucleotide and the probe are selected from the group consistingof DNA, cDNA, RNA, mRNA, rRNA, tRNA, PNA, a DNA-like molecule or anRNA-like molecule. In any of the embodiments disclosed herein or anycombination thereof, the binding of said probe to said polynucleotidecan be detected by gel electrophoresis, hybridization, PCR, qPCR, ornucleotide sequencing.

A challenge inherent in the use of binding probes to detect specific Tcells is the low binding affinity between the peptide:MHC complex andthe TCR. Here, in one embodiment, the polynucleotide-peptide conjugateis multimerized or oligomerized, which overcomes the low bindingaffinity issue. In one embodiment, branched adapter molecules are usedto produce multivalent conjugates in which several identical peptidesare covalently linked to a single identifying DNA tag. In one aspect,conjugates that each contain two identical peptides are produced anddetected. This approach can be readily adapted to higher ordermultiplexing in preferred embodiments. In another preferred embodiment,the method is performed in a high throughput fashion.

In one example, T cell lines HA1.7 and 131.5 are used. HA1.7 and 131.5are known to recognize the peptides PKYVKQNTLKLAT (SEQ ID NO: 6) andQYIKANSKFIGITE (SEQ ID NO:7), respectively, in complex with HLA-DR1(Hennecke and Wiley, 2002, J Exp Med. 4: 571-581; De Magistris et al.,1992, Cell. 68: 625-634). Conjugates with sequences PKYVKQNTLKLAT (SEQID NO: 6) and QYIKANSKFIGITE (SEQ ID NO: 7) are prepared at valencies of1, 2 and 4. The conjugates are then incubated together withrecombinantly-expressed HLA-DR1. In addition, HA1.7 and 131.5 T cellsare added to the binding reactions, either from the outset or after aninitial period of peptide-MHC binding. After incubation, cells arewashed to remove unbound species (these could include conjugates, MHCmolecules, and MHC:conjugate complexes) and then the bound conjugateseluted and detected by their cDNA tags. In one embodiment, afterestablishing a T cell detection capability, two T cell lines arecombined in different ratios to confirm the sensitivity and multiplexityof the assay. In another embodiment, both types of conjugates areapplied simultaneously as detectors to confirm the sensitivity andmultiplexity of the assay.

In the method of the invention, the T cell receptor can be a T cellreceptor for which it is desired to identify the peptide epitoperecognized by the receptor. In one aspect, the T cell receptor is from apatient with a T cell-mediated disease, such as an autoimmune disease ora hyperproliferative disease. In other embodiments, the target T cellreceptor is from a patient with a different condition, such as aninfection by a pathogenic microorganism or a patient with cancer.Knowledge of the antigen that is bound by a specified T cell can havetherapeutic value for a variety of reasons. Preferably, the T cellreceptor is an αβ T cell receptor. An αβ T cell (expressing an αβ T cellreceptor) is a lineage of T lymphocytes found in mammalian species andbirds that expresses an antigen receptor (i.e., a TCR) that includes anα chain and a β chain. Without being bound by any theory, the T cellreceptor can be a γδ T cell receptor.

The T cell receptor can be expressed by a cell or provided as a solubleT cell receptor. In the former embodiment, the T cell receptor can beexpressed by the T cell that naturally expresses the receptor (e.g., a Tcell clone or hybridoma) or by another cell that recombinantly expressesthe T cell receptor. In the latter embodiment, the soluble T cellreceptor is preferably immobilized on a substrate or solid support forcontact with the MHC and the polynulcoetide-peptide conjugate.

Briefly, a substrate or solid support refers to any solid organicsupports, artificial membranes, biopolymer supports, or inorganicsupports that can form a bond with a soluble T cell receptor withoutsignificantly affecting the ability of the T cell receptor to bind to anMHC-peptide complex for which the T cell receptor has specificity.Exemplary organic solid supports include polymers such as polystyrene,nylon, phenol-formaldehyde resins, acrylic copolymers (e.g.,polyacrylamide). Exemplary biopolymer supports include cellulose,polydextrans (e.g., Sephadex™), agarose, collagen and chitin. Exemplaryinorganic supports include glass beads (porous and nonporous), stainlesssteel, metal oxides (e.g., porous ceramics such as ZrO₂, TiO₂, Al₂O₃,and NiO) and sand. Soluble T cell receptors can be bound to a solidsupport by a variety of methods including adsorption, cross-linking(including covalent bonding), and entrapment. Adsorption can be throughvan del Waal's forces, hydrogen bonding, ionic bonding, or hydrophobicbinding. Exemplary solid supports for adsorption immobilization includepolymeric adsorbents and ion-exchange resins. Cross-linking to a solidsupport involves forming a chemical bond between a solid support and theT cell receptor. Cross-linking commonly uses a bifunctional ormultifunctional reagent to activate and attach a carboxyl group, aminogroup, sulfur group, hydroxy group or other functional group of thereceptor to the solid support. Entrapment of involves formation of,inter alia, gels (using organic or biological polymers), vesicles(including microencapsulation), semipermeable membranes or othermatrices, such as by using collagen, gelatin, agar, cellulosetriacetate, alginate, polyacrylamide, polystyrene, polyurethane, epoxyresins, carrageenan, and egg albumin.

The target T cell receptor can be labeled with a detectable label.Detectable labels suitable for use include any compound detectable byspectroscopic, photochemical, biochemical, immunochemical, electrical,optical or chemical means. Useful labels in the present inventioninclude biotin for staining with labeled streptavidin conjugate,magnetic beads (e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein,texas red, rhodamine, green fluorescent protein, and the like),radiolabels (e.g., ³H, ¹²⁵I, ³⁵S, ¹⁴C, or ³²P), enzymes (e.g., horseradish peroxidase, alkaline phosphatase and others commonly used in anELISA), and colorimetric labels such as colloidal gold or colored glassor plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.

As used herein, “TCR recognition” or “TCR binding”refers to the abilityof a TCR to bind to an MHC-peptide complex, wherein the level ofbinding, as measured by any standard assay (e.g., an immunoassay orother binding assay), is statistically significantly higher than thebackground control for the assay. Binding assays are well known in theart. For example, a BIAcore machine can be used to determine the bindingconstant of a complex between two proteins. The dissociation constantfor the complex can be determined by monitoring changes in therefractive index with respect to time as buffer is passed over the chip.Other suitable assays for measuring the binding of one protein toanother include, for example, immunoassays such as enzyme linkedimmunoabsorbent assays (ELISA) and radioimmunoassays (RIA), ordetermination of binding by monitoring the change in the spectroscopicor optical properties of the proteins through fluorescence, UVabsorption, circular dichrosim, or nuclear magnetic resonance (NMR).

In one embodiment, one can additionally measure whether a T cellreceptor that is expressed by a T cell, when bound by an MHC-peptidecomplex produced by the invention, displays a T cell response to thebinding. A T cell response occurs when a TCR recognizes an MHC proteinbound to an antigenic peptide, thereby altering the activity of the Tcell bearing the TCR. As used herein, a “T cell response” can refer tothe activation, induction of anergy, or death of a T cell that occurswhen the TCR of the T cell is bound by an MHC-peptide complex. As usedherein, “activation” of a T cell refers to induction of signaltransduction pathways in the T cell resulting in production of cellularproducts (e.g., interleukin-2) by that T cell. “Anergy” refers to thediminished reactivity by a T cell to an antigen. Activation and anergycan be measured by, for example, measuring the amount of IL-2 producedby a T cell after and MHC-peptide complex has bound to the TCR. Anergiccells will have decreased IL-2 production when compared with stimulatedT cells. Another method for measuring the diminished activity of anergicT cells includes measuring intracellular and/or extracellular calciummobilization by a T cell upon engagement of its TCRs. As used herein, “Tcell death” refers to the permanent cessation of substantially allfunctions of the T cell. In the method of the present invention, the Tcell will typically encounter the MHC-peptide complex in the absence ofadditional costimulatory signals that are normally required to induce Tcell activation events. However, under some conditions, some type orlevel of T cell response will be measurable.

The ability of a T lymphocyte to respond to binding by an MHC-peptidecomplex can be measured by any suitable method of measuring T cellactivation. Such methods are well known to those of skill in the art.For example, after a T cell has been stimulated with an antigenic ormitogenic stimulus, characteristics of T cell activation can bedetermined by a method including, but not limited to: measuring theamount of IL-2 produced by a T cell (e.g., by immunoassay or biologicalassay); measuring the amount of other cytokines produced by the T cell(e.g., by immunoassay or biological assay); measuring intracellularand/or extracellular calcium mobilization (e.g., by calcium mobilizationassays); measuring T cell proliferation (e.g., by proliferation assayssuch as radioisotope incorporation); measuring upregulation of cytokinereceptors on the T cell surface, including IL-2R (e.g., by flowcytometry, immunofluorescence assays, immunoblots); measuringupregulation of other receptors associated with T cell activation on theT cell surface (e.g., by flow cytometry, immunofluorescence assays,immunoblots); measuring reorganization of the cytoskeleton (e.g., byimmunofluorescence assays, immunoprecipitation, immunoblots); measuringupregulation of expression and activity of signal transduction proteinsassociated with T cell activation (e.g., by kinase assays,phosphorylation assays, immunoblots, RNA assays); and, measuringspecific effector functions of the T cell (e.g., by proliferationassays, cytotoxicity assays, B cell assays). Methods for performing eachof these measurements are well known to those of ordinary skill in theart, and all such methods are encompassed by the present invention.

In one embodiment, methods disclosed in any embodiments or combinationsthereof can be used for vaccine design or vaccine development. Whilevaccines are best established in the infectious disease context,development efforts have more recently broadened their focus toanti-tumor vaccines, as well as tolerogenic vaccines for the treatmentof allergy and autoimmunity. Whereas traditional vaccines are based onwhole pathogens (either killed or attenuated), modern approaches(so-called “second” and “third generation” vaccines) have focused onimmunogen subunits (particular proteins or peptides), as these offer themajor advantages of reduced risk, improved stability and, mostimportantly, the opportunity for more refined control over the immuneresponse. The present invention provides methods for developing asuccessful subunit vaccine, that is, for selecting epitopes on thesubunit(s) to be efficiently presented to T cells as MHC-bound peptides.

In one embodiment, the entire proteome of the immunogen of interest(e.g. bacterial or viral pathogen) is represented as peptide-cDNAconjugates. These conjugates are incubated, in a single binding pool,with HLA molecules from vaccinee populations (either at a representativelevel or, in a personalized medicine approach, at the individual level).The competitive binding reaction is then select the best binders fromthe pool, in a way that broadly mimics the natural antigen processingmilieu in vivo, and these binders are reported in a sensitive andhigh-throughput fashion by next generation sequencing. The same approachcould also be used to discover useful peptide-MHC tetramer combinations,and thereby provide ways to investigate and monitor T cell immuneresponses. In another embodiment, the methods disclosed herein are usedfor developing protein-based therapeutics, for example, forpre-screening therapeutics against patient HLA molecules, in order toavoid protein sequences with the potential to elicit adverse reactions.

In one aspect, the application of the peptide-MHC binding assaydisclosed herein involves the use of genotype-based MHC sets derivedfrom patient samples, e.g., peripheral blood from a patient or a normalcontrol. Since the MHC molecules are cell surface-expressed proteins, inone aspect, the assay format involves using intact cells as a solidsupport capable of capturing and separating binding MHC-peptide probes,e.g., a polynucleotide-peptide conjugate disclosed herein. In oneembodiment, the polynucleotide-peptide conjugates are incubated withcells, the cells are pelleted and washed to wash away unbound and/ornon-specifically bound polynucleotide-peptide conjugates, and then thepolynucleotide-peptide conjugates that remain bound to the cells afterthe washing are eluted and quantified. In some embodiments, allexpressed MHC proteins on the surface of cells are available for theassay at their physiological abundances without the need for capture bya panel of MHC-binding antibodies. In other embodiments, the methoddisclosed herein avoids exposing internal cellular components to thepolynucleotide-peptide conjugates (the peptide probes), which may bindnon-specifically to the internal cellular components. In someembodiments, cell-surface components other than MHC molecules areremoved, blocked, or masked, for example, to prevent non-specificbinding to the polynucleotide-peptide conjugates. Peptide binding tocell-surface expressed MHC has been demonstrated in the art, see forexample Ceppellini et al., “Binding of labelled influenza matrix peptideto HLA DR in living B lymphoid cells,” Nature 1989, 339: 392-4, thedisclosure of which is incorporated herein by reference in its entiretyfor all purposes.

The following exemplary embodiments and examples are intended to furtherdescribe and illustrate various aspects of the invention, but not tolimit, the scope of the invention in any manner, shape, or form, eitherexplicitly or implicitly.

The present invention is further illustrated by the following exemplaryembodiments:

1. An MHC-binding peptide conjugated to a polynucleotide.

2. A library of at least two MHC-binding peptides each conjugated to apolynucleotide, wherein each said polynucleotide is identified by aprobe that specifically binds to said polynucleotide.

3. A composition comprising at least two MHC-binding peptides eachconjugated to a polynucleotide, wherein the at least two MHC-bindingpeptides are multimerized or oligomerized.

4. The composition of embodiment 3, wherein the at least two MHC-bindingpeptides are conjugated to the same polynucleotide and are thusmultimerized or oligomerized.

5. The composition of embodiment 3, wherein the at least two MHC-bindingpeptides are each conjugated to a separate polynucleotide, wherein thepolynucleotides mediate the multimerization or oligomerization of the atleast two MHC-binding peptides.

6. The composition of embodiment 5, wherein the mediation is throughnucleotide sequence complementarity.

7. A method for detecting binding of a peptide to an MHC molecule,comprising:

contacting said MHC molecule with a polynucleotide-peptide conjugate,said polynucleotide-peptide conjugate comprising said peptide and apolynucleotide;contacting said polynucleotide-peptide conjugate with a probe thatspecifically binds to said polynucleotide;detecting binding of said probe to said polynucleotide; andcorrelating binding of said probe to said polynucleotide with binding ofsaid peptide to said MHC molecule.

8. A method for simultaneously detecting binding of a library ofpeptides to an MHC molecule, comprising:

providing a polynucleotide-peptide conjugate for each said peptide, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide;contacting said MHC molecule with a pool of said polynucleotide-peptideconjugates;contacting each of said polynucleotide-peptide conjugate with a probethat specifically binds to each said polynucleotide;detecting binding of said probe to each corresponding polynucleotidethat each said probe specifically binds; andcorrelating binding of said probe to each corresponding polynucleotidewith binding of each corresponding peptide to said MHC molecule.

9. A method for detecting in a library of peptides competitive bindingof each said peptide to an MHC molecule, comprising:

providing a polynucleotide-peptide conjugate for each said peptide, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide;contacting said MHC molecule with a pool of said polynucleotide-peptideconjugates;contacting each of said polynucleotide-peptide conjugate with a probethat specifically binds to each said polynucleotide;detecting binding of said probe to each corresponding polynucleotidethat each said probe specifically binds; andcorrelating binding of said probe to each corresponding polynucleotidewith binding of each corresponding peptide to said MHC molecule,wherein said peptides compete for binding of said MHC molecule.

10. A method of embodiment 8 or 9, further comprising comparing bindingof each said peptide to said MHC molecule, among the peptides in saidlibrary.

11. A method of detecting binding of a peptide to a TCR, comprising:

contacting said TCR with an MHC molecule and a polynucleotide-peptideconjugate, said polynucleotide-peptide conjugate comprising said peptideand a polynucleotide;contacting said polynucleotide-peptide conjugate with a probe thatspecifically binds to said polynucleotide;detecting binding of said probe to said polynucleotide; andcorrelating binding of said probe to said polynucleotide with binding ofsaid peptide to said TCR.

12. A method for simultaneously detecting binding of a library ofpeptides to a TCR, comprising:

providing a polynucleotide-peptide conjugate for each said peptide, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide;contacting said TCR with a pool of said polynucleotide-peptideconjugates and an MHC molecule;contacting each of said polynucleotide-peptide conjugate with a probethat specifically binds to each said polynucleotide;detecting binding of said probe to each corresponding polynucleotidethat each said probe specifically binds; andcorrelating binding of said probe to each corresponding polynucleotidewith binding of each corresponding peptide to said TCR.

13. A method for detecting in a library of peptides competitive bindingof each said peptide to a TCR, comprising:

providing a polynucleotide-peptide conjugate for each said peptide, saidpolynucleotide-peptide conjugate comprising said peptide and apolynucleotide;contacting said TCR with a pool of said polynucleotide-peptideconjugates and an MHC molecule;contacting each of said polynucleotide-peptide conjugate with a probethat specifically binds to each said polynucleotide;detecting binding of said probe to each corresponding polynucleotidethat each said probe specifically binds; andcorrelating binding of said probe to each corresponding polynucleotidewith binding of each corresponding peptide to said TCR,wherein said peptides compete for binding of said MHC molecule and saidTCR.

14. The method of any one of embodiments 11-13, wherein said TCR isselecting from the group consisting of a TCR on a T cell, a soluble TCR,an isolated TCR, and an immobilized TCR.

15. The method of any one of embodiments 7-14, further comprisingcomparing the detected binding of said peptide to said MHC molecule orsaid TCR with a reference.

16. The method of embodiment 15, further comprising selecting thedetected binding of said peptide over the reference, for the purposes ofidentifying antigens in infection, autoimmunity, allergy, or cancer, orfor vaccine design.

17. The method of any one of embodiments 7-16, wherein thepolynucleotide and the probe are selected from the group consisting ofDNA, cDNA, RNA, mRNA, rRNA, tRNA, PNA, a DNA-like molecule or anRNA-like molecule.

18. The method of any one of embodiments 7-17, wherein the binding ofsaid probe to said polynucleotide is detected by gel electrophoresis,hybridization, PCR, qPCR, or nucleotide sequencing.

19. The method of any one of embodiments 7-18, wherein the MHC moleculeis immobilized.

20. The method of any one of embodiments 7-19, wherein saidpolynucleotide-peptide conjugate is multimerized or oligomerized.

21. The method of any one of embodiments 7-20 performed in a highthroughput fashion.

22. The method of any one of embodiments 7-20, which further comprisesone or more of the steps of:

allowing binding between the polynucleotide-peptide conjugate and theMHC molecule to reach equilibrium; washing the complex between thepolynucleotide-peptide conjugate and the MHC molecule under a suitablecondition to remove unbound or non-specifically boundpolynucleotide-peptide conjugate; allowing the complex between thepolynucleotide-peptide conjugate and the MHC molecule to dissociate; anddetecting the polynucleotide-peptide conjugate that remains bound to theMHC molecule.

23 The method of embodiment 22, wherein the complex between thepolynucleotide-peptide conjugate and the MHC molecule is allowed todissociate in the presence of one or more blocker species.

24. The method embodiment 23, wherein the one or more blocker speciesprevent binding or reassociation of the polynucleotide-peptide conjugateto the MHC molecule.

25. The method embodiment 23 or 24, wherein the blocker species competewith the polynucleotide-peptide conjugate for binding to the MHCmolecule, and the binding between the blocker species and the MHCcomplex does not generate a signal indicative of specific bindingbetween the polynucleotide-peptide conjugate and the MHC molecule.

26. The method of any one of embodiments 7-25, wherein the binding ofthe polynucleotide-peptide conjugate to the MHC molecule occurs in thepresence of one or more chaperons.

27. The method of embodiment 26, wherein the chaperon is selected fromthe group consisting of a protein chaperon, a chemical chaperon, HLA-DMand an analogue thereof, a small molecule that has the same or similarchaperon function as HLA-DM, parachlorophenol (pCP) and an analoguethereof, and dimethylsulphoxide (DMSO) and an analogue thereof

EXAMPLE 1 Production of Peptide-cDNA Conjugates

Peptide-cDNA conjugates can be produced from DNA molecules by eitherCoA-mediated formation or puromycin-mediated formation. Each method canbe implemented at high plexity, for example by using high-complexitymicroarrays as a source of DNA templates.

CoA-Mediated Formation

In this method, the reactions are conducted in one isolated compartmentper sequence. As illustrated in Table 1 (left), peptide-cDNA conjugatesare formed from DNA templates comprising the following elements (from 5′to 3′): (i) a T7 promoter, (ii) a 5′ UTR sequence containing ribosomalbinding site (RBS), (iii) a sequence encoding variable peptide (flankedby spacer residues), (iv) a sequence encoding S6 tag, and (v) a stopcodon. In a single incubation mixture, these DNA templates aretranscribed to form mRNAs, the mRNAs translated into peptides, and themRNAs and peptides covalently attached to each other. Peptide-mRNAattachment occurs through a polyfunctional adapter molecule comprising aDNA hairpin (with an overhang region complementary to the conserved 3′end of the transcribed mRNAs) that is covalently attached, by means of apolyethylene glycol (PEG) linker moiety, to a coenzyme A (CoA) molecule.Attachment of mRNA to adapter is mediated by T4 DNA ligase, andattachment of peptide to adapter occurs by SFP synthase-mediatedattachment of the CoA molecule to the S6 tag. Peptide-mRNA conjugatesare then converted to peptide-cDNA conjugates using reversetranscriptase, followed by treatment with RNAse to degrade mRNA.Prepared peptide-cDNA conjugates are then isolated from the reactionmixture by capture onto beads bearing DNA baits complementary to aconserved DNA sequence present in all conjugates. As an optional furtherpurification step, SFP synthase along with an excess of biotinylated S6peptide, is added to bead-captured species. In this reaction, speciescontaining unreacted CoA molecules are biotinylated and then depleted bymeans of streptavidin beads.

Puromycin-Mediated Formation

This method does not require that the reactions be conducted in oneisolated compartment per sequence. As previously described (Kozlov etal., 2012, PLoS One 7: e37441) and illustrated in Table 1 (right),peptide-cDNA conjugates are formed from DNA templates comprising thefollowing elements (from 5′ to 3′): (i) a T7 promoter, (ii) a 5′ UTRsequence containing ribosomal binding site, (iii) a sequence encodingvariable peptide (flanked by spacer residues), (iv) a stop codon, and(v) a 3′ UTR region. To form conjugates, DNA templates are transcribedto form mRNA. The mRNA is then purified and attached to a polyfunctionaladapter molecule comprising a DNA molecule (with a region complementaryto the conserved 3′ end of the transcribed mRNAs) that is covalentlyattached, by means of a linker moiety, to a puromycin molecule. Theresulting adapter-mRNA conjugates are purified and then translated toform peptide-mRNA conjugates. The ribosomes mediate attachment betweenthe newly-formed peptides and the puromycin molecule of the associatedadapter-mRNA conjugates. Peptide-mRNA conjugates formed in this way arethen converted to peptide-cDNA conjugates by the addition of reversetranscriptase, followed by treatment with RNAse to degrade mRNA.Prepared peptide-cDNA conjugates are then isolated from the reactionmixture by capture onto beads bearing DNA baits that are complementaryto a conserved DNA sequence present in all conjugates.

EXAMPLE 2 Multimerization of Peptide-cDNA Conjugates

This example describes representative methods for multimerization ofpeptide-cDNA conjugates. The preparation schemes described in Example 1can be modified to enable applications that require multivalentpeptide-cDNA conjugate molecules. These approaches for multimerizationof peptide-cDNA conjugates can also be implemented in conjunction witheach other to enable even higher order multiplexing.

Multimerization Mediated by Multivalent Adapters

In this approach, the adapter molecule that mediates the connectionbetween peptide and mRNA is modified to include multiple peptide capturemolecules. For example, the capture molecule is CoA in the case ofCoA-mediated formation, and the capture molecule is puromycin in thecase of puromycin-mediated formation. Multiple peptides are attached toa single mRNA molecule during the peptide-cDNA synthesis process.

To form a bivalent adapter for CoA-mediated formation, a DNA hairpincomprising amino-modifications on two of the bases is used. These sitesare reacted with NHS-ester groups on bifunctional PEG crosslinkermolecules. The other functionality of the PEG crosslinker, maleimide, isattached to CoA by reacting with an excess of CoA trilithium salt. Theresulting doubly-PEGylated, doubly-CoA-modified adapter is purified bygel electrophoresis, and used as the adapter in the peptide-cDNAsynthesis protocol described in Example 1.

Multimerization by Hybridization

In this approach, peptide-cDNA conjugates are prepared in such a waythat multiple conjugates can associate with each other by nucleic acidhybridization to form a multivalent conjugate. Various implementationsare possible. In one implementation, DNA templates can be designed withcomplementary tag sequences so that they form hybrid pairs when mixed(implementation 1 of Table 2). In an alternative implementation, afraction of the peptide-mRNA conjugate preparation can be retained andthen mixed together with subsequently-formed peptide-cDNA conjugates(implementation 2 of Table 2). In alternative implementations,multimerization is mediated by separate linker DNA templates containingmultiple complementary regions (implementations 3 and 4 of Table 2).

EXAMPLE 3 Peptide-MHC Binding Assay

To test the binding of different peptides to MHC, peptide-cDNAconjugates were incubated overnight with biotinylated MHC molecules andthen the MHC molecules were captured onto streptavidin-bearing beads.The beads were washed to remove unbound species, and then the remaining,MHC-bound peptide-cDNA conjugates were eluted under denaturingconditions and detected by gel electrophoresis, qPCR and/or DNAsequencing.

In the experiment shown in FIGS. 4A-4B, peptide-cDNA conjugates wereproduced by CoA-mediated formation as described in Example 1 with thefollowing sequences: YKTIAFDEEARR (SEQ ID NO: 1) and YPKYVKQNTLKLAT (SEQID NO: 2). These sequences were derived from the proteomes ofMycobacterium Tuberculosis and Influenza A virus, respectively. Theywere selected because they are known to bind respectively to the MHCclass II molecules HLA-DR3 and HLA-DR1, without cross-binding (Sidney etal., 2002, J Immunol. 169: 5098-5108). Biotinylated HLA-DR3 and HLA-DR1monomers were incubated overnight with the YKTIAFDEEARR (SEQ ID NO: 1and YPKYVKQNTLKLAT (SEQ ID NO: 2) peptide-cDNA conjugates (as describedin Sidney et al., 2001, Curr. Protoc. Immunol. Chapter 18: Unit 18.3),immobilized using streptavidin beads, washed 3 times with PBST, and thebinding conjugates then eluted for analysis by gel electrophoresis andquantitative polymerase chain reaction. The results shown in FIGS. 4A-4Bindicate that the eluted peptide-cDNA conjugates were detected by bothreadouts, and that each conjugate bound to the expected MHC molecule butnot to the other HLA-DR family member.

In the experiment shown in FIG. 5, peptide-cDNA conjugates with thesequences YPKYVKQNTLKLAT (“YP (WT)”) (SEQ ID NO: 3), YPKYVKQNTLKLAA (“YP(T14A)”) (SEQ ID NO: 4), and YPKAVKQNTLKLAT (“YP (Y4A)”) (SEQ ID NO: 5)were produced. Peptides of YP (WT), YP (T14A), and YP (Y4A) are known tobind the HLA-DR1 molecule with high, high, and low affinities,respectively. These three conjugates were then incubated, eitherindividually (1-plex) or mixed together in equal quantities (3-plex),with biotinylated HLA-DR1 monomers and then eluted and analyzed by qPCRas described above. FIG. 5 shows that the expected profile of bindingfor the three conjugates (high, high, low) was detected, both in thecase where conjugates were present individually (1-plex), and in thecase where the conjugates were incubated and detected as a mixture(3-plex).

EXAMPLE 4 Peptide:MHC-T Cell Binding Assay

To quantify different T cell specificities, multivalent peptide-cDNAconjugates can be incubated overnight with MHC molecules as in Example 3above. The resulting incubation mixture contains multivalentpeptide-cDNA conjugates where each peptide is bound to an MHC molecule“probe,” unbound peptide-cDNA conjugates, and unbound MHC molecules. Theresulting incubation mixture is then applied to a biological samplecontaining T cells. After a period of incubation, cells are pelleted andwashed to remove species that do not bind to the T cells. Bound speciesare then eluted and detected by gel electrophoresis, qPCR and/or DNAsequencing.

EXAMPLE 5 Peptide-MHC Binding Assay

In this example, a 14-mer peptide (SEQ ID NO: 2, “YP”) from theinfluenza virus, known to bind the MHA molecule HLA-DRB1*01:01, waschemically coupled to a 50-mer DNA oligonucleotide of a definedsequence. As shown in FIGS. 6A-6C, after purification, the resulting YPconjugate was incubated in the presence (“DR1”) or absence (“beadsonly”) of recombinant HLA-DRB1*01:01, then captured with beads bearinganti-HLA-DR antibody (L243), washed, eluted and then detected by qPCRreaction using primers specific for the attached DNA.

Shown in FIGS. 6A-6C are the qPCR results for 3 sequential experiments(i), (ii), and (iii). FIG. 6A shows qPCR results of experiment (i) underdifferent incubation temperatures and times. FIG. 6B shows qPCR resultsof experiment (ii) using different concentrations of YP conjugate asinput to the incubation. FIG. 6C shows qPCR results of experiment (iii)using fresh tubes for the elution.

Based on the results in experiment (i), the 37° C./16hr incubationcondition was fixed in experiments (ii) and (iii). Based on the resultsin experiment (ii), 18 pM was fixed in experiment (iii), being aconcentration in the range of those achievable for a single species in acomplex conjugate pool. Experiment (iii) shows that, under theseconditions, a ˜100-fold enrichment of YP conjugate binding to DR1 overbeads is achieved when fresh elution tubes are used.

EXAMPLE 6 Detection of Specific Peptide:MHC Binding Among a Pool ofPolynucleotide-Peptide Conjugates

A pool of ˜4000 custom-designed peptide-cDNA conjugates were designedusing a publicly-available dataset of HLADRB1*01:01 binders (availableat: http://bio.dfci.harvard.edu/DFRMLI/datasets/IEDB_DRB1_0101.htm) andsynthesized using puromycin technology. Peptides “YP” (14-mer, SEQ IDNO: 2) and “YK” (12-mer, SEQ ID NO: 1) which are known to bind or notbind the MHA molecule HLA-DRB1*01:01, respectively, and each bearing adistinct 50-mer DNA oligonucleotide, were admixed to the ˜4000-plex setat concentrations comparable to other members of the library, togenerate a second pool. The resulting pools were applied in the assay asdescribed in FIGS. 6A-6C, using either beads only or the HLA moleculeDR1.

Shown are qPCR results for primer sets specific for YP (FIG. 7A), YK(FIG. 7B) and the puromycin pool (FIG. 7C). Whereas the specificconjugate (YP) is enriched ˜1000-fold among the admixed pool in the DR1condition compared to beads only (as shown in FIG. 7A), no suchenrichment is observed for the non-DR1-specific conjugate (YK) (as shownin FIG. 7B). The pool itself was also enriched ˜1000-fold in the DR1condition compared to beads only (as shown in FIG. 7C).

EXAMPLE 7 Detection of Specific Peptide:MHC Binding by Extension

A 12-mer peptide (SEQ ID NO: 1, “YK”) from M Tuberculosis, known to bindthe MHA molecule HLA-DRB1*03:01, was chemically coupled to a 50-mer DNAoligonucleotide of a defined sequence. The MHC binding assay describedin FIGS. 6A-6C was performed (“standard format”), or with the additional“extension assay format” depicted in FIG. 8A. In this extension format,the bead-bound anti-HLA-DR antibody (“L243”) was conjugated to a ˜40-merDNA tag that included a 3′ 7-mer sequence complementary to last 7 basesof the YK DNA tag. After washing, DNA polymerase was added to extend thetags, and product was detected using a qPCR primer set specific for theextension product.

Shown in FIG. 8B are qPCR results for both the extension assay formatand standard format, at the indicated concentrations of antibody. Theresults indicate that the extension assay format is capable of producing˜1000-fold enrichment of the YK signal in the DR1 condition compared tobeads only.

All headings are for the convenience of the reader and should not beused to limit the meaning of the text that follows the heading, unlessso specified.

Citation of the above publications or documents is not intended as anadmission that any of them is pertinent prior art, nor does itconstitute any admission as to the contents or date of thesepublications or documents.

While various embodiments of the invention have been described above, itshould be understood that they have been presented by way of exampleonly, and not by way of limitation. Likewise, the various diagrams maydepict an example architectural or other configuration for thedisclosure, which is done to aid in understanding the features andfunctionality that can be included in the disclosure. The disclosure isnot restricted to the illustrated example architectures orconfigurations, but can be implemented using a variety of alternativearchitectures and configurations. Additionally, although the disclosureis described above in terms of various exemplary embodiments andimplementations, it should be understood that the various features andfunctionality described in one or more of the individual embodiments arenot limited in their applicability to the particular embodiment withwhich they are described. They instead can, be applied, alone or in somecombination, to one or more of the other embodiments of the disclosure,whether or not such embodiments are described, and whether or not suchfeatures are presented as being a part of a described embodiment. Thusthe breadth and scope of the present disclosure should not be limited byany of the above-described exemplary embodiments.

Sequence Listing

SEQ ID NO Sequence 1 YKTIAFDEEARR 2 YPKYVKQNTLKLAT 3 YPKYVKQNTLKLAT 4YPKYVKQNTLKLAA 5 YPKAVKQNTLKLAT 6 PKYVKQNTLKLAT 7 QYIKANSKFIGITE

1-5. (canceled)
 6. A plurality of complexes, wherein each complexcomprises a polynucleotide-peptide conjugate and a majorhistocompatibility complex (MHC) molecule, wherein the polynucleotide ofeach polynucleotide-peptide conjugate is covalently attached to thepeptide and uniquely identifies the peptide, and wherein in eachcomplex, the peptide of the polynucleotide-peptide conjugate binds tothe MHC molecule.
 7. The plurality of complexes of claim 6, comprisingat least 100 different peptides.
 8. The plurality of complexes of claim6, comprising at least 1,000 different peptides.
 9. The plurality ofcomplexes of claim 6, comprising at least 10,000 different peptides. 10.The plurality of complexes of claim 6, comprising at least 100,000different peptides.
 11. The plurality of complexes of claim 6, whereinthe polynucleotide of each polynucleotide-peptide conjugate is selectedfrom the group consisting of DNA, RNA, PNA, a DNA-like molecule, and anRNA-like molecule.
 12. The plurality of complexes of claim 6, whereinthe peptides of the polynucleotide-peptide conjugates are syntheticallyproduced peptides.
 13. The plurality of complexes of claim 6, whereinthe peptides of the polynucleotide-peptide conjugates are randomlygenerated peptides.
 14. The plurality of complexes of claim 6, whereinthe peptides of the polynucleotide-peptide conjugates comprise antigensselected from the group consisting of autoantigens, cancer antigens,infectious agents, toxins, and allergens.
 15. The plurality of complexesof claim 6, wherein the polynucleotide of each polynucleotide-peptideconjugate comprises a nucleic acid molecule encoding the peptide of thepolynucleotide-peptide conjugate.
 16. The plurality of complexes ofclaim 15, wherein the nucleic acid molecule is a cDNA.
 17. The pluralityof complexes of claim 6, wherein the peptide is about 5 to about 40amino acid residues in length.
 18. The plurality of complexes of claim6, wherein the peptide is about 8 to about 20 amino acid residues inlength.
 19. The plurality of complexes of claim 6, which is in asolution.
 20. A method, comprising: (1) contacting a T-cell receptor(TCR) with the plurality of complexes of claim 6; (2) separating one ormore polynucleotide-peptide conjugate bound to the TCR from one or morepolynucleotide-peptide conjugate not bound to the TCR; and (3)determining a sequence of the polynucleotide of eachpolynucleotide-peptide conjugate bound to the TCR, thereby identifyingcomplex formation of the TCR and the peptides of the complexes.
 21. Themethod of claim 20, wherein in the contacting step, the TCR isimmobilized on a substrate.
 22. The method of claim 20, wherein theseparating step comprises washing away the one or morepolynucleotide-peptide conjugate not bound to the TCR.
 23. The method ofclaim 20, wherein in the contacting step, the TCR is soluble.
 24. Themethod of claim 23, wherein the separating step comprises immobilizingthe soluble TCR on a substrate.
 25. The method of claim 24, wherein theseparating step further comprises washing away the one or morepolynucleotide-peptide conjugate not bound to the TCR.
 26. The method ofclaim 20, wherein in the contacting step, the TCR is on a T cell. 27.The method of claim 26, wherein the separating step comprises pelletingthe T cell.
 28. The method of claim 27, wherein the separating stepfurther comprises washing away the one or more polynucleotide-peptideconjugate not bound to the TCR.
 29. The method of claim 20, wherein thedetermining step is performed using nucleic acid sequencing.
 30. Themethod of claim 29, wherein the nucleic acid sequencing is highthroughput DNA sequencing.